yves a. lussier, md, fellow acmi (elected) - the lussier … · yves a. lussier, m.d. 3 29-aug-14...

Yves A. Lussier, M.D. 1 8.29.2014

Yves A. Lussier, MD, Fellow ACMI (Elected)

Dept. of Medicine The University of Arizona

USA • tel: • fax: email: [email protected]

http://www.lussierlab.org/ http://www.linkedin.com/in/lussier

Table of Content

Education and Training .......................................................................................................... 2 Academic Training .......................................................................................................... 2 Predoctoral Research Training ........................................................................................ 2 Post-Doctoral Training (traineeship) ............................................................................... 2 Licensure ......................................................................................................................... 2 Board Certifications ......................................................................................................... 2

Academic and Clinical Appointments .................................................................................... 2 Academic & Medical Center Leadership and Administrative Appointments ........................ 3

Medical Center & University Governance ...................................................................... 3 Quality of Care and Patient Safety .................................................................................. 3 Information Technology and Technology Transfer Positions ......................................... 3 Translational Bioinformatics ........................................................................................... 4

Corporate Leadership and Professional Activities ................................................................. 4 Company Founder ........................................................................................................... 4 Senior Leaderships: Board of Directors, President or VP ............................................... 4

Press Coverage ....................................................................................................................... 6 Conference Founder ............................................................................................................... 7 Editorial Boards, Scientific Review Boards, Journal and Grant Review Committees .......... 7 Service to Organizations and Societies .................................................................................. 8 Membership to Societies and Associations ............................................................................ 9 Intellectual Property ............................................................................................................. 10 Teaching Experience and Responsibilities ........................................................................... 10 Faculty Advisory Committee and/or Mentorship ................................................................. 11 Grants, Scholarship, Fellowship Support and Contracts ...................................................... 14 Publications and Communications ....................................................................................... 16

Journal Publications ....................................................................................................... 16 Refereed Conference Papers .......................................................................................... 22 Original knowledge bases .............................................................................................. 23 Editorial and Perspectives ............................................................................................. 23 Scientific Reviews ......................................................................................................... 24 Invited Conference Papers ............................................................................................. 24 Book Chapters ............................................................................................................... 24 Published Refereed Abstracts and Refereed Conference Panels ................................... 25 Invited Scientific and Grand Round Lectureships ......................................................... 33 Intramural Lectures ........................................................................................................ 36 Tutorials and Workshop Presentations .......................................................................... 38

Yves A. Lussier, M.D. 29-Aug-14 2

Yves A. Lussier, MD, Fellow ACMI 5050 S Lake Shore Dr, #1214, Chicago, IL 60615 USA

Phone: 773 614-3736 • Email: [email protected] Physician and Surgeon Permanent License, Province of Quebec

Education and Training Academic Training 1985 B. Engineering, Faculty of Applied Sciences, University of Sherbrooke, PQ, Canada 1989 M.D., Faculty of Medicine, University of Sherbrooke, PQ, Canada Predoctoral Research Training 1982-3 Research Student, Dept. Medicine (Mentor: L. Tétreault, MD PhD), Univ. of Sherbrooke, Canada 1986-8 Research Student, Dept. Human Physiol. (Mentor: G. Plante MD PhD), Univ. of Sherbrooke Post-Doctoral Training (traineeship) 1989-1990 Internship, Laval University Hospital, Quebec, Canada 1990-2 Resident in Family Medicine, University of Sherbrooke Med Ctr (http://www.chus.qc.ca/en/), Canada 1998-2001 Post-Doc. Res. Fellow, Dept. Biomed. Informatics, College Surgeons & Physicians, Columbia Univ.

(mentors: James J Cimino, MD; Carol Friedman, PhD). Licensure 1985 Quebec Professional Engineering License 1989-present License of the Medical Council of Canada 1991-present Full Medical License, College of Physicians of Quebec 1998-2007 Full Medical License, College of Physicians and Surgeons of Ontario 2001-6 Full Medical License, Office of the Professions, State of New York Board Certifications 1991 Board Certified, College of Family Physician of Canada

Academic and Clinical Appointments Academic Departments Appointments 01/ 1994- 08/ 2001 University of Sherbrooke

• Adjunct Professor of Family Medicine, (sabbatical leave: 1998-2001) 01/ 1995- 08/ 2001 University of Sherbrooke Clinical Research Center

• Associate Researcher 09/ 2001- 12/ 2005 College of Physicians and Surgeons, Columbia University, New York, New York.

• Assistant Professor of Biomedical Informatics (2001-5) • Assistant Professor of Medicine (2002-5)

01/ 2006- 07/ 2011 The University of Chicago • Associate Professor of Medicine (Section of Genetic Medicine)

08/ 2011- 11/ 2013 University of Illinois at Chicago • Professor of Medicine, of Bioengineering and of Biopharmaceutical Sciences

12/ 2013- present University of Arizona • Professor of Medicine • Statistics Graduate Interdisciplinary Program

Medical Centers Employment 01/ 1992- 12/ 2000 Attending Physician (hospitalist, ER, and intensive care), Hôtel-Dieu Hospital of

Sherbrooke (1992-7), Integrated to the University of Sherbrook Medical Center (Centre Hospitalier Universitaire de Sherbrooke - CHUS; 1997-2000).

01/ 1992- 09/ 1999 Medical Staff, Vimy Clinic (’92-96), St-Vincent Clinic (’96-99), Sherbrooke, Canada. 01/ 2001- Attending Physician, Emergency Medicine Department, Windsor Hospital, QC, Canada. 05/ 2002- 12/ 2005 Attending Physician, Medicine Dept, Columbia Un. Medical Ctr & New York Presbyt Hosp Academic Institutes Appointments 2007-2011 Fellow, Computation Institute, Argonne National Laboratory


2007-present Fellow, Inst. for Genomics & Systems Biol (IGSB), Argonne National Laboratory 2008-2011 Member, Ludwig Center for Metastasis Research 2013-present Member, BIO5

Academic & Medical Center Leadership and Administrative Appointments Medical Center & University Governance 1994-7 Board Director, “Governance Board of Physicians, Dentists & Pharmacists”; University of

Sherbrooke Medical Ctr (http://www.chus.qc.ca/en/; 2535 hospital beds) • Role: governance of the medical center (operation budget & quality of care), six Directors • 1994-7 Centre Hospitalier Hôtel - Dieu de Sherbrooke (HDS) 1994-7, • 1996-7 Co-conceived and led the contractual agreements for the integration of four hospitals.

This creative strategy resulted in a 50% cost-reduction of operation budget in 2 years mandated by the Federal and Provincial Goverments.

2011-2103 Chief Research Information Officer (CRIO) & Assist. Vice President for Health Affairs, Univ. of Illinois Hosp. & Health Sciences System (UIHHSS)

2012 Recruitment Committee for 3 Assoc. Vice-Presidents and 2 Assistant Vice-Presidents; UIHHSS 2011-2103 Chief Knowledge Officer (Associate Vice President), Univ. of Arizona Health Sciences (UAHS)

Quality of Care and Patient Safety 2001-3 New York Presbyterian Hospital (http://nyp.org/) Patient Safety Committee 2003-5 New York Presbyterian Hospital Clinical Alert Committee (VigiLENS Clinical Event Monitor) 2012 Tissue Bank Committee, University of Illinois Hospital System 2012-2013 Intensive Care Unit Quality Improvement Committee, UIHHSS

Information Technology and Technology Transfer Positions - Medical Centers & Hospitals 1990-1 Hospital EMR Advisor to the CIO, University of Sherbrooke Medical Ctr (Health Data System

Ulticare http://www.healthdatasystems.com/; mainframe capacity plan & laboratory order lists) 1994-5 Design of the Pathology Module of the Ulticare EMR in partnership with Health Data Systems

and Dr. Roger Côté (role: “postcoordinated” information models development for SNOMED 3.0 Topology, Morphology & Diagnoses implemention) ; University of Sherbrooke Medical Ctr.

2002-5 Clinical Event Monitor Leader, IT Clinical Informatics Operations Committee of the New York Presbyterian Hospital (http://nyp.org/) and the Columbia Presbyterian Medical Center.

2007-11 Service Oriented-Architecture (SOA) Governance Working Group, Univ of Chicago Medical Ctr 2008-11 The Board of Computing Activities and Services (BCAS), The University of Chicago 2011-2013 Information Technology Governing Council – Research Committee, Un. of Illinois at Chicago 2011-2013 Chief Information Officers Committee, University of Illinois

- University Information Systems 1991-2 Planning and Evaluation Committee of the pan-Canadian risk register for primary care led by the

Dept. of Family Medicine of University of Sherbrooke (FAMUS). 2006-7 Ad hoc member (2006) and consultant (2007) for promotion of informaticians faculty,

Committee on Appointments and Promotions (CAOP), University of Chicago. 2006-8 Biological Science Division Information Services Advisory Committee, University of Chicago 2006-9 Chair, Velos Clinical Trial Mgmt System Advisory Committee, Univ of Chicago BSD 2006-9 Chair, Biomed Inform. Facility Advis. Comm, Shared Research Facilities, Univ Chicago BSD 2006-2011 Director, Center for Biomedical Informatics, Dept. of Medicine, University of Chicago 2007 Recruitment Committee for the Director of the Microarray Facility, Univ of Chicago BSD Cores 2007-2011 Initiative in Biomed Inform (IBI) Advisory Committee, Univ of Chicago BSD 2011-2013 Encore Clinical Trial Mgmt System implementation, University of Illinois Cancer Cetner 2012-2013 Committee for UIHHSS (https://hospital.uillinois.edu/) EMR Selection (responses to RFP)


-University Technology Transfer

2001-6 Clinical & Adj. Assoc. Dir., Ctr for Adv. Inform. Mgmt, Columbia Univ. (http://www.cat.columbia.edu/) 2008-10 UChicagoTech Faculty Advisory Committee (http://tech.uchicago.edu/); Un. of Chicago.

Translational Bioinformatics 1-Academic Research Centers and Institutes 2004-6 NLP & Ontology Lead, Columbia Center for Comput. Biology and Bioinformatics (C2B2) 2006-present Fellow, Computation Institute of The Argonne National Laboratory 2007-present Fellow, Inst. for Genomics & Systems Biol (IGSB), Argonne National Laboratory. 2008-11 Member, Ludwig Center for Metastasis Research 2011-13 Academic Dir. for Biomedical Informatics, Research Resource Ctr, Univ. of Illinois at Chicago 2011-13 Director (joint), Institute for Interventional Health Informatics (I2HI), Univ. of Illinois at Chicago

2- Clinical Translational Science Awards 2006-11 Dir., ITM Biomedical Informatics Core (co-Director from 2006-2010), University of Chicago

Institute for Translational Medicine (UC-ITM) 2007 Committee Member, CTSA Biomedical Informatics Core Advisory Committee, UC-ITM 2007-11 Committee Member, CTSA Executive Committee, UC-ITM 2008-11 Informatics Education Director, Committee on Clinical and Translational Science, UC-ITM 2011-13 Assoc. Dir. for Informatics, Ctr for Clinical and Translat. Science (CCTS), Univ. of Illinois

3- Cancer Centers 2006-11 Assoc. Director for Informatics, Comprehensive Cancer Ctr, Univ. of Chicago (UCCCC) 2006-11 Investigator, Program 4: Clinical and Experimental Therapeutics, UCCCC 2006-11 Member of the UCCCC Executive Committee 2011-13 Assoc. Director for Informatics, Cancer Ctr, Univ. of Illinois at Chicago

4- Northeast Research Center of Excellence in Biodefense and Emerging Infectious Diseases (NBC-Northeast Biodefense Center, NIAID-funded)

2003-6 Governance Board Member ↳portal 2003-6 Director, Biomedical Informatics Research and Service Core

Education Steering Committees 1983-4 Executive Board of the School of Engineering, University of Sherbrooke, Canada 1985-6 Executive Board of the School of Medicine (reporting to Dean Gilles Pigeon), University of

Sherbrooke, Canada 1986 Undergrad Medical Studies Revision Committee, School of Medicine, Univ of Sherbrooke 2011-13 Transdisciplinary PhD in Health Informatics Planning Committee, University of Ill. at Chicago

Corporate Leadership and Professional Activities Company Founder 1991 Development Purkinje Inc. http://www.Purkinje.com, founder with R St-Arneault, PP Yale & Y Levesque • 1993 DPI Product: Dossier tablet-based CPOE-enabled EMR used in 3000 clinics & hospitals • 1994 DPI merged with “Purkinje” 1994 Accurate Informatics and Medicine consulting (AIM) Senior Leaderships: Board of Directors, President or VP 1992-5 Board of Directors, Purkinje Inc. (pen-based electronic medical records) 1982-3 President, Engineering Student Association (http://www.ageg.ca/); University of Sherbrooke, Canada. 1991-3 Senior VP of Research and Development and of International Affairs, Purkinje.com. • Conceived and completed 3 investment plans totaling $18,000,000 (2nd -4th rounds of funding). • Managed $4,000,000 R&D budget over four years (~40 employees; 65,000 term DAG/ontology).


Professional 1982-4 Analyst & programmer (part time; Dr. L. Tétreault, MD PhD.), Dept. Medicine, Univ of Sherbrooke.

Developed a clinical trial mgmt & statistical system used in 3 distinct trials phase 3a and 3b. 1982–4 IBM Canada, Comp Analyst & Product Engineer, 16-month (4 internships), Québec & Toronto, Consulting 1994-5 Scientific advisor, Hoechst Marion Roussel, Clinidata Division. 1997-8 Scientific advisor, Purkinje.com. 1983-8 Consultant, medical and pharmaceutical informatics, • YAL, Inc. (1983-1993), • Accurate Informatics and Medicine Inc. (1993-1998). 1999-2001 Consultant, Ctr for Advanced Information Mgmt & Columbia Innovation Enterprise, Columbia Un.

Honors 2005 Inducted Fellow American College of Medical Informatics (ACMI)

http://www.amia.org/about-amia/leadership/acmi-fellow/yves-lussier-md-facmi

2004 1st Awardee, Columbia University Faculty Mentoring Award, Biomedical Sciences and Graduate School of Arts and Science, http://home.uchicago.edu/~lussier/FacultyMentoringAward-Lussier.jpg

2003-4 Three IBM Faculty Awards for the VigiLENS event monitor (6/15/2003; 12/22/2003, 6/9/2004) http://www.cumc.columbia.edu/news/in-vivo/Vol3_Iss08_july_04/around_and_about.html

1998 Competitive Research Fellowship (3 awardees), Medical Research of Canada

Scientific Publication Awards 2012 American Medical Association (AMA) Research Symposium, “overall winner”

AMIA Annu Symp Proc. 2012;2012:1040-9.

2012-13 Two “Best Paper” Awards, Translational Bioinformatics Conference (TBC) • 2013/10: N-of-1-pathways” unveils personal deregulated mechanisms from a single pair of RNA-seq samples: towards

precision medicine. J Am Med Inform Assoc 2014 online http://www.lussierlab.net/publications/Lab-Awards/Award_TBC.pdf • 2012/10: J Am Med Inform Assoc 2013 Jul 1;20(4):619-29. http://www.lussierlab.org/publications/Lab-Awards

2008-12 Five “Outstanding/Distinguished Paper” Awards, American Medical Informatics Association (AMIA) • 2011/10: J Am Med Inform Assoc. 2012 Mar-Apr;19(2):295-305 http://www.amia.org/news-and-publications/amia-enews/e-news-november-17-2011 • 2010/3: BMC Bioinformatics. 2010 Oct 28;11 Suppl 9:S11http://lussierlab.org/publications/Lab-Awards/AMIA-2010.pdf

• 2009/3: BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S6 http://lussierlab.org/publications/Lab-Awards/XinanYang.pdf • 2008/3: BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:S11 http://lussierlab.org/publications/Lab-Awards/Lussier-2008-award.pdf • 2008/3: BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:S8 http://lussierlab.org/publications/Lab-Awards/Lee-Sam-amia_award.pdf

Scientific Publication Highlighted at Conferences

2010-13 (AMIA/STB)

one of 25 Best Translational Bioinformatics Papers of the Year” recognition, from the Closing Keynote of the American Medical Informatics Association’s Summit on Translational Bioinformatics • 2010/3: PLoS Comput Biol 2010 6(4): e1000730. https://dl.dropbox.com/u/2734365/amia-tb-review-10.pdf • 2013/3: J Am Med Inform Assoc. 2012 Mar-Apr;19(2):306-16 https://dl.dropbox.com/u/2734365/amia-tb-review-13.pdf

2007-13 (ISCB / ISMB)

Three “Highlights of the Year” paper recognition, International Society for Computational Biology (ISCB) at their Annual Meeting (ISMB) • PLoS Comput Biol, 2006;2(11):1419-35. http://www.iscb.org/cms_addon/conferences/ismbeccb2007/program/highlights.html

• PLoS Comput Biol 2010;6(4): e1000730. http://www.iscb.org/cms_addon/conferences/ismbeccb2011/highlights.php • PLoS Comput Biol 2012;8(1):e1002350. http://www.iscb.org/cms_addon/conferences/ismbeccb2013/highlights.php

Corporate awards 1994 Two awards, Fédération de l’Informatique du Québec (>2,500 members, > 1,100 organizations).

As VP of clinical R&D at Purkinje Inc. for the Innovation and excellence of the electronic medical record: Dossier


• “Octas of Excellence”, http://www.actionti.com/octas-1994 • “Octas of Innovation”, http://www.actionti.com/accueil/octas/historique-des-octas/octas-de-l-excellence

Student Scholarships & Awards 1983 IBM engineering student award 1984 Best mechanical engineering student (Quebec Iron and Titanium Corp.) 1986-7 Twice “best graduate research scholar” at Univ. Sherb. (1986,1987, Fond Recherche Sci. Québec – FRSQ)

Commencement and Conference Keynote Lectureships (14) 2001 • State University of New York Downstate Medical Center, Commencement Speaker, Medical

Information Systems Technology (MIST) Program, New York, Oct 16 2002 • Annual Meeting of the Canadian Institute for Health Information (CIHI), Opening Keynote, Quebec. 2003 • Special Libraries Association Conference, Keynote Speaker, New York, NY. 2004 • Columbia University PhD Convocation Faculty Address, “The Subculture of One’s Specialty in

Graduate Studies”, 5/17/2004. 2006 • NIH National Library of Medicine, Annual Investigator’s Address to the Board of Regents.

“Collecting Phenotypic Information from Multiple Databases for Correlation with Genomics”. http://www.nlm.nih.gov/od/bor/2-06bor.pdf

2009 • IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIP) “Using Phenomic Networks for Therapeutic Target and Biomarker Discovery”. http://syen.ualr.edu/gensips2009/

2010 • 1st Congress of Personalized Medicine, Shanghai. Keynote Speaker, http://www.bitlifesciences.com/mdpm2010/ • Wellcome Trust Sanger Inst. & EU Bioinform. Inst.(EBI) 1st CALB Workshop on the Collaborative

Annotation of a Large Biomedical Corpus Challenge. “Quantized phenotypes emerge as multiscale mechanisms underpinning complex traits”. Cambridge, UK. http://www.ebi.ac.uk/Rebholz-srv/CALBC/workshop1/

2011 • Asia Pacific Bioinformatics Conference (APBC 1/2011) Seoul, Korea http://www.snubi.org/workshop • Network Tools and Applications in Biology (NETTAB 10/2011); http://www.nettab.org/ Pavia, Italy. “Network Models of Mesophenotypes in Personal Genomics and Targeted Therapies”

• Ann. Symp. on Syst. Biol., Korean Society for Mol. & Cellular Biol., Jeju, Korea http://www.ksmcb.or.kr/eng/ 2013 • 4th International Conference on Biomedical Ontology (ICBO 2013), “Personalised therapeutics

powered by ontology transforms”, Montreal, Canada, 8 & 9 July • 3rd Translational Bioinformatics Conference (TBC 2013), “Personalome: clinically actionable 'Omics ” Seoul, Korea, Oct 3-5th. Keynote Speaker

Press Coverage 2006 • “Bioinformatics Tool-Related Papers of Note”, October 2006 (published Nov 17th), BioInform

http://www.genomeweb.com/informatics/bioinformatics-tool-related-papers-note-october-2006 2008 • Some Diabetics Don’t Have What They Thought They Had” by Andrew Pollack,

The New York Times, May 6, http://www.nytimes.com/2008/05/06/health/research/06hist.html?ref=research • “Phenotype Lookup and Linkup: New Methods Arise to Mine Phenotypes for Gene Function”, BioInform, Sept. 5, Vivien Marx. http://www.genomeweb.com/informatics/phenotype-lookup-and-linkup-new-methods-arise-mine-phenotypes-gene-function

2009 •“A cancerous melody” by Jet Akst, The Scientist, Sept. 25. http://www.the-scientist.com/blog/display/55998/ •“Talks at AMIA Summit Signal Progress in linking Clinical and Biomedical Informatics” BioInform, March 20, Vivien Marx. http://www.genomeweb.com/talks-amia-summit-signal-progress-linking-clinical-and-biomedical-informatics?page=3

•“Streamlining the Language of Genetic Medicine” by Robert Mitchum, University of Chicago Faculty Focus, Oct.19, 2009. http://pages.exacttarget.com/page.aspx?QS=472529ec60bdf32a666588374c54c4f033b3dcda813a7f4b

2010 • “Researchers Show Gains in Finding Reusable Drugs”, Wall Street Journal, Aug. 18th 2010. Amy Dockser Marcus. http://online.wsj.com/article/SB10001424053111903639404576514542144726276.html

• Computer Analysis Could Find New Uses for Existing Drugs, iHealthBeat, Aug. 18th 2011


http://www.ihealthbeat.org/articles/2011/8/18/computer-analysis-could-find-new-uses-for-existing-drugs.aspx 2011 •“Studies Describe Expression-based Strategy for Finding New Uses for Existing Drugs” GenomeWeb

Daily , Aug. 17th. http://www.genomeweb.com/informatics/studies-describe-expression-based-strategy-finding-new-uses-existing-drugs 2013 •“Seasoned Drugs Offer Therapeutic Gold Mine / Drug repositioning”, Genetic Engineering &

Biotechnology News, VOl 33, No 10, p.1,18-19. May 15. Caitlin Smith http://gen.epubxp.com/i/127418/19 • Sequencing papers of note, In Sequence, March 05, http://www.genomeweb.com/sequencing/print-last-weeks-sequencing-related-papers-note-57?page=2

• >4,600 Clinical Societies portals and news portal citing JAMIA 2013 paper on ICD10. Conference Founder 2007 MSCBB - Midwest Symposium on Computational Biology and Bioinformatics

• Founding co-chair and member of the Scientific Program Committee in 10/6/2007. 2008 Ontology of Cellular Networks, Newark, NJ 3/26-27 (with B Smith & A Ruttenberg), NIH funded 2008 Cancer Informatics Symposium, University of Chicago Comprehensive Cancer Center 2008 AMIA STB- AMIA Summit on Translational Bioinformatics (Founding Session Chair)

• 2009: Conference Chair and Chair of the Scientific Program Committee • 2010-present: Conference Advisor and Ramoni Award Committee Member

2009 ICBO - International Conference on Biomedical Ontology (Founding Scientific Committee) ↳portal 2011 TBC- Translational Bioinformatics Conference (Founding Organizing Committee Member)

Editorial Boards, Scientific Review Boards, Journal and Grant Review Committees NIH/ National Library of Medicine 2005-6 Long Range Plan 2006-16 (Panel 4): Support for Genomic Science of the 21st Century, ↳portal 2011-present BLIRC- The Biomedical Library and Informatics Review Committee (NLM grant reviews)

Associate & Guest Editor of Journals 2005-7 Associate Editor, CBM, Computers in Biology and Medicine, Elsevier 2008 Guest, BMC Bioinformatics 10(2008),Proc.. of the 2008 Summit on Translat. Bioinform 2009 Guest, BMC Bioinformatics 10(2009), Proc. of the 2009 Summit on Translat. Bioinform 2009-10 Guest, J of Biomed Inform 42(2009), Special Issue on Method. for Translational Bioinformatics 2012-present Associate Editor, BMC Bioinformatics ↳portal Editorial Boards 1993-5 CMI - Canadian Medical Informatics Journal 2003-7 SNOMED International Editorial Board, College of American Pathologists 2006-present JBI- Journal of Biomedical Informatics, Elsevier 2007-9 IHTSDO (SNOMED)- Internat. Health Terminology Std Develop.Org ↳portal 2008-present Genomics Insights, Libertas Academica 2010-present JAMIA- Journal of the American Medical Informatics Association (British Medical J Group) 2010-present JPM - Journal of Personalized Medicine ↳portal 2011-present In Silico Biology (IOS Press), ↳portal Scientific Advisory Boards 2002-4 Board of Directors, Medical Informatics and Technology Applications Consortium (MITAC), a NASA Space Partnership Development. Board of Directors, NASA/MITAC Med Inform & Technol Applications Consortium 2002-4 McGill “Infostructure de Recherche Intégrée en Santé du Québec” (IRIS) 2003-5 First Genetic Trust 2004-7 Cerner Corp. (Ontology Board) ↳portal 2005-6 IBM Healthcare & Life Sc., Primary Academic Partner of IBM Center for Computat Medicine 2006 University of Chicago Lung SPORE application 2008-2011 Consortium Neuropsychiatric Phenomics (annual review) ↳portal 2009 Collaborative Annotation of a Large Biomedical Corpus ↳portal 2010 Elect. Med. Record Peer Review Panel; for: President, Univ. of TX M.D. Anderson Cancer Ctr.


2010-present Worldwide Innovative Networking (WIN) in Personalized Cancer Medicine ↳portal 2013-present Mouse Genome Database (MGD) Advisory Board (Janan Eppig, PI;) ↳portal 2013 Genome Canada & Genome BC Research Oversight Committee (Andrew Peen & Francis Lau PIs) 2013-present IPSEN Pharmaceuticals, ↳portal Grant Review Committees

2002-5 CAT Grant Review Committee, Columbia Center for Advanced Technology 2003 NSF TATRC Grant Review Panel, “Information Technology Research” Medium Panel, 4/28-30/03 2003 TATRC Homeland Security Product Line Review, Telemed and Adv Technology Research Ctr 8/5/03 2003 NIGMS MIDAS, Pilot projects for models of infectious disease agent study, 11/12-3/03. 2006 NIH CSR, Biodata Management and Analysis (BDMA), 6/12-13/06 6/4-5/07 2007 The Israel Science Foundation (ISF), Phenomic Applications 2009 NIH/NLM Ad Hoc Committee reviewing the EUREKA grants (RFA-GM-09-008.html) 2009 Mail Reviewer. ZRG1 OTC-K (58) RC1 COI 2009 Risk, Prevention & Health Behavior IRG , National Institutes of Health CS 11/13/09 2011 Indiana Ctr for Syst. Biol. & Personal. Med., for: Vice Chancellor for Research, Indiana Univ. (IUPUI). 2011 NIGMS NIH National Institute of General Medical Sciences. Ad hoc review of the Glue Grants.

Journal Manuscript Review - Clinical Journals: • Annals Internal Med • Clin Pharmacol & Therap • Drug Discov. Today • Expert Rev. Mol. Diag. • J Clin Oncol • J of Pain • Lancet • Lancet Diabet & Endoc • Lancet Infect Dis • Lancet Neurol • Lancet • Respir Med • New England Journal of Medicine (NEJM) • Science Translational Medicine (STM) - Biological Journals: • Cancer Research • Molecular Systems Biology • Nature Biotechnology • PLoS ONE • Proceed. National Academy of Science (PNAS) • Protein - Genetics, Genomics and other molecular scale Journals: • BMC Medical Genomics • BMC Genomics • Drug Discovery Today • Genetic Epidemiology • Genome Biology • Genome Med. • Genomics • Genome Res. • Human Molecular Genetics • Nucleic Acids Research (NAR) • Physiological Genomics • Pharmacogenet. & Genomics • Proteomics - Informatics (Bio- and Clinical), Computational Biology and Computer Science Journals: • Applied Ontology • Artificial Intelligence in Medicine • BMC Bioinformatics • BMC Medical Informatics and Decision Making • Bioinformatics • Briefings in Bioinformatics • Canadian J. Med Inform • Cancer Informatics • Computers in Biology and Medicine • Cancer Informatics • Internat J Medical Informatics • Computer Methods and Programs in Biomedicine • J Am. Medical Informatics Assoc. (JAMIA) • J Biomed. Informatics (JBI) • J Bioinf. & Compt. Biol. (JBCB) • J Decision Support Systems • PLoS Computational Biol. • PROTEINS: Structure, Function & Bioinf

Service to Organizations and Societies

Workshops Organizer RCSPC Royal College of Surgeons and Physicians of Canada. Chair and Organizer: 8 hr Workshop on Comput

& Internet Literacy for Physicians. Annual meetings: • Halifax, 9/26/1996 • Vancouver 9/25/1996. Scientific Program Committees Memberships AMIA American Medical Informatics Association (Yearly Conf.: Fall & Summit on Transl. Bioinformatics)

• 2007, SPC Member, Foundations of Informatics Track, Chicago, Fall Symposium • 2008, Founding Session Chair, co-organizer and member of Scientific Program Committee • 2009, Conference Chair and Chair of the Scientific Program Committee • 2010 SPC Member, AMIA Fall Annual Symposium, Wash DC • 2010,-11,-12: member of the STB Senior Advisory Committee • 2014 Steering Committee Member for AMIA’s 2014 Health Policy Invitational: Personalized


Medicine: Next Generation Informatics Opportunities and Challenges BIOKDD 8th Internat. Wrkshp Data Mining in Bioinform, 2008, Las Vegas ↳portal BOA Biomedical Ontology in Action, 12/8/06, Baltimore. DILS Int.Conf. Data Integr. Life Sciences , ↳portal • 2012, • 2013 ECCB European Conf. on Computational Biology • 2005 ↳portal GIW Language Biol & Med & 18th Genome Inform. Wrkshp, Singapore 12/5-6/07 ↳portal HEALTHINF HEALTHINFO 2012 HISC IEEE-Healthcare Inform., Imaging and Syst. Biology, • Prog. Committee (SystBiol track), 27/9/2012 ICBO International Conference on Biomedical Ontologies ↳portal

(formerly SOFG: Standards & Ontologies for Functional Genomics) • 2009 Member of the Founding Organizing Committee and Scientific Committee • 2010 Scientific Committee

ICMLA Int. Conf. on Machine Learning and App.: Machine Learning, App. Bioinformatics & Comput. Biol, • 2009, -10, -11, SPC Member

InCoB 12th Intern. Conf. on Bioinform. of the Asia-Pacific Bioinform. Network • 2013, SPC Member ↳portal ISMB International Conference on Intelligent Systems for Molecular Biology • 2007 ↳portal • 2008, ↳portal KRMED "Representing and sharing knowledge using SNOMED" Int.l Health Terminology Stds Devel.

Org.(IHTSDO) & KRMED Wrk Grp on Formal (Bio-)Med. Knowledge Repr.of AMIA. Phoenix, 2008 NETTAB Network Tools and Applications in Biology

• 2011 Clin. Bioinform., Pavia • 2012 Integrated Bio-Search, Milan ↳portal PSB Pacific Symposium on Biocomputing

Track Chair • 2005, • 2008, • 2009 ; Review Committees: 2005, 2008, 2009, 2012 RECOMB RECOMB DREAM-SB; Conf. Syst. Biol., Regul. Genom. & Reverse Engineer., ↳portal • 2010 • 2012 TBC Translational Bioinform. Conf., Founding Editorial Board Member, SPC member: • 2011 • 2012 • 2013 Conference Session Chair 2005 AMIA Annual Symp, Session 28-Natural Language Processing, 10/24. ↳portal 2006 PSB, Session "Towards a Semantic Web for Biology" ↳portal 2008 AMIA Summit on Translational Bioinformatics, ↳portal Conference Proceedings Review • AMIA Fall Symposium, • Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) • Knowledge Representation in Medicine (KR-MED), • European Conference on Computational Biology (ECCB) • Medinfo Proceedings • Pacific Symposium on Biocomputing (PSB) Conference Committee Membership

1991-2003 PSG-06 Committee of the Computerized Patient Record Work Group of AMIA 1994-2003 Family Medicine Informatics Committee of AMIA 1999-2003 Inform. Work. Party the World Org. of Nation. Colleges, and Acad. Assoc. Fam. Phys. (WONCA). 2003-present Clinical genomics working group, AMIA PhD Thesis Defence Committee 2007 Ying Tao, Columbia University 2011 Lee Sam, University of Michigan Honors Thesis Defence Committee Columbia University (2001-6): A dozen candidates to the MSc and MA programs. University of Chicago (2011): Ah Rume (Julie) Park, Kelly Regan (5/5/11).

Membership to Societies and Associations 1985-9 CCPE Canadian Council of Professional Engineers 1992-6 CRCQ Clinical Research Society of Quebec (Club de Recherche Clinique du Quebec) 1991-8 COACH Canadian Medical Informatics Association


1993-5, 2012-present IEEE Institute of Electrical and Electronics Engineers 1989-2007 CMA Canadian Medical Association 1990-present AMIA American Medical Informatics Association 2005-present ACMI American College of Medical Informatics (Inducted Fellow) 2007-present ISCB International Society for Computational Biology 2010-present SCTS The Society for Clinical and Translational Science 2011-present AACR The American Society for Cancer Research 2012-present HIMSS Healthcare Information and Management Systems Society 2012-present AAPS The American Association of Pharmaceutical Scientists 2012-present AAAS The American Association for the Advancement of Science 2012-present ASHG The American Society for Human Genetics

Intellectual Property • Provisional patent application, • Patent 12/498,898: methods and systems for Extracting Phenotypic Information from the Literature via natural

Language processing (C Friedman, YA Lussier, L Ena) -2009/7/7 (, baker Botts LLP file# 070050.3791) • Patent 20060074991 - System and method for generating an amalgamated database. Clinigene. Internat. Patent

App. PCT/US03/35470, filed 11/6/03, published as WO 2004/044818 on 6/2/04, priority claims to provis. U.S. app.#60/424,728, filed November 6, 2002. Lussier YA, Cantor M, Sarkar IN. App#: 11/120,715

• Terminological Map. Continuation-In-Part of Internat.Patent App#PCT/US03/35470. Lussier YA, Li J (2003). • Invention report on DynaTreeviewer, Liu HF, Lussier YA, Friedman A (2002). • Invention report on Phenogene Discovery System, Friedman A, Lussier YA, (2004). • Invention report on viral database Palacios, Liu, Jabado, Briese, Hegi, Lussier, Lipkin WI. (2004). (GreeneChip). • Invention on an oligonucleotide microarray for the detection of all known vertebrate viruses. Palacios G, Liu

Y, Briese T, Lussier YA, Lipkin WI (2005). • Invention report on Phenogene Viewer, Tao Y, Lussier YA, Friedman C (2004). • Invention report on Nondeterministic Model Theoretic Mapping between Heterogeneous Databases, Lussier

YA, Li J (2004). • Invention report on Flat Treeviewer. Sam L, Lussier YA. (2005) • Invention report on User-Directed Pearls of Knowledge. Lussier YA, Sam L, Borlawsky T. (2005). • Invention report on VigiLENS server-based and ontology-driven event monitor (2005), Lussier YA, Shortliffe

EH, Li J, Kamasumadram N, Hripcsak G, Cimino J, Forman B, Wajngurt D, Johnson J, Sengupta S.

Teaching Experience and Responsibilities Clinical teaching

1991-6 Clinical Instructor in Family Medicine, Ctr Hospital. Hôtel-Dieu de Sherbrooke, University of Sherbrooke, 1994-8 Clinical Instructor, Department of Family Medicine, University of Sherbrooke, Canada. 2002-5 Clinical Instructor, Department of Medicine, Columbia University Informatics Courses

- Columbia University (Dept. Biomedical Informatics) 1999 Invited Lecturer. History of standard coding systems, G4020 Representation of Medical Data, 1/29/99 1999 Invited Lecturer. “Software Project Management”, G4098 Topics In Medical Informatics, 11/99 1999 Invited Lecturer. “Basic Web Design Techniques”, G4030 User Interfaces in Medicine, 8/4/99 1999 Invited Lecturer. “Advanced Web Design Techniques”, G4030 User Interfaces in Medicine, 8/11 2001 Invited Lecturer. “Pen-based Computing”, G4030 User Interfaces in Medicine, April 27 2001-4 Course Director, G4099. Research Seminars, Department of Biomedical Informatics (50 students). 2003-5 Course Director, G4055 Decision Support in Biomedicine, (24 students).


2003-4 Module Instructor: Intro to Biomed. Informatics, BMEN E1001x Engineering In Medicine, Dept. of Biomed. Engineer., Fu Foundat. School of Engineer. & Appl Sc, Columbia University, 10/27/03, 11/ 8/04.

2004 Module Instructor: G4099. “Computational approaches to high throughput analyses of non-molecular phenotypes” Research Seminars, (55 students), 2/17/04

2004-5 Course co-Director: Methods in Biomedical Informatics (G4002), (25 students). 4 Modules: Theories on Biological Data, Reasoning and Logic, Biological Ontologies, Knowledge Engineering.

- The University of Chicago 2007 Module Instructor: “Genomic approaches to accelerate the discovery and translation

of biomedical knowledge” 10/4/07, BIOS 25406 “Translational Biomed Research, from bench to bedside”. 2008 UCCRC Research Seminars in Cancer Informatics, Lecturer: Dr. Lynn H Vogel (CIO of MD Anderson)

[2008/9/26). http://uccrc.uchicago.edu/docs/Aug%20Sept%208-12%20(3).pdf 2009 Module Instructor: “Translational Molecular Bioinformatics” 5/14/09, BIOS 25406 “Translational

Biomedical Research, from bench to patient bedside”. 2009 Module Instructor: “genomics in Cancer” 12/2/09, “12/7/09” Bioinformatics Analyses in Cancer” CABI

30800 “Cancer Biology 1: Human Cancer Presentation and Modeling”. 2010 Seminar. Computational Phenomics and Thorough Biological Characterization Uncovers a Novel Tumor

Suppressor microRNA and its Regulatory Network. The IGSB Fellows Series. 5/20/10. 2010 Course Director. Personal Genomics and Translational Bioinformatics. (BIOS 27100, CCTS 42100) 2011 Module Instructor: “Bioinformatics in Cancer” 24/5/11, Cancer Biology 3: Signal Transduction and Model

Organisms (CABI 31200; NPHP 31200; CPHY 31200). . - The University of Illinois at Chicago

2012 Seminar, Medical Scientist Training Program 2012 Informatics Colloquium of the Dept. of Health Informatics, University of Illinois at Chicago, 2012 UIC Bioengineering Seminar, University of Illinois at Chicago 2013 Center for Pharmaceutical Biotechnology Seminar Series, University of Illinois at Chicago 2013 Institute for Pulmonary Respiratory Medicine Seminar Series, University of Illinois at Chicago

-Other 1986 Module Instructor. Tétreault L, Lussier YA, Biostatistics Course - Masters in Experimental Medicine, School of Medicine, University of Sherbrooke 1991 Invited Course Director (3 weeks, 6 days/wk) to Faculty members. “Designing & programming databases”. School of Medicine, University of Bangui, Central African Republic.

Faculty Advisory Committee and/or Mentorship K-award Mentor for --Funded K Awards-- • Ankit Desai, MD, 2011-present, Assoc Prof University of Arizona (2014-present) Assistant Prof. of Medicine, Univ of Illinois at Chicago (2011-13) • Roberto Machado, MD, 2009-2012, Associate Prof. of Medicine, Univ of Illinois at Chicago • Younghee Lee, PhD, Res. Assoc (Assist. Prof.), Dept. of Medicine, 2010-2013 (K awarded in 2011) • Huiping Liu, PhD, MD, PhD R. Assist. Prof. Univ of Chicago (K99 CA160638-01, 2012/9-2013). • Frederico Innocenti, MD, PhD, 2008-10, Assoc. Prof. Pharmacotherapeutics, UNC Eshelman Sch. Pharm. --Application for K Awards by Faculty members -- • Kain Khalpey, MD, PhD, Assoc Prof of Surgery, University of Arizona, K23 ; 2014. • Julio Duarte, Pharm D, Assist. Prof., Dept. of Pharmaceutical Sc, Univ Ill Chicago, 2013 • Pritesh Patel, MD, Assist. Prof., Dept. of Medicine, Univ Ill Chicago, 2012-2013 • Lucy Chen, MD, Assist. Prof., Dept. of Medicine, Univ Ill Chicago, 2011-2013 • James Chen, MD, 2011-12 (Assist. Prof of Biomedical Inform., College of Medicine , Ohio State University) • Yang Xiang, PhD, 2012-13 (Assist. Prof of Biomedical Inform., College of Medicine, Ohio State University) • Xiang “Holly” Yang, PhD, 2012-13 (Res. Assist. Prof, The University of Chicago, K-22 PA-10-195)


• Peter H. O’Donnell, MD, 2010-11, Assistant Professor of Medicine, Univ of Chicago • Dana Elderson, MD, 2009-11, Assist, Prof, of Med,, University of Chicago (Advis. Commit.; K award appl.) • Sam Volchenboum, MD, PhD, 2007-11, Assist Prof. Ped. Hem-Onc, Dir. Ped. Inform., Univ. of Chicago (K08) • Michael Grassi, MD, 2006-2010, Assist. Prof. Ophthal., Univ. Ill.at Chicago (mentor on submitted K award) • Liliana Moreno, PhD, 2008-10, Res. Assist. Prof., Dept. of Med., Univ. Ill. at Chicago (mentor, sub. K- award) • Andy Minn, MD, PhD, 2007, Assist. Prof. Rad. & Cell. Oncol., Univ. of Pennsylvania, (mentor, K award appl.) --Application for K Awards by Fellows -- • Tomas Nuño, Ph.D., Post Doctoral Fellow of Pharmacy, University of Arizona (K01) ; 2014. • Joel Pekow, MD, Fellow, Section of Gastroenterology, 2009-2011, Univ of Chicago (K8 award). • Ankit Desai, MD, 2006-10, Resident in Cardiology, Univ of Chicago (prelim. studies, K-award)

Faculty Advisory Committee or Faculty Mentorship for Independent Researchers • Andrew Boyd MD, Res. Assist. Prof., Dept. of Health Informatics, UIC, 2012-2013 • Michael Maitland, MD, Assistant Professor Hemato/Oncology, 2007-2011 (redaction of grants) • Eneida Mendonça, MD, PhD, Associate Professor, Dept. of Medicine, 2007-10 • Sameer Badlani, MD/MBBS, Fellow Med Informatics, Instructor , Medicine, Sect. of Hospitalist Med., 2007-8 • Edwin Posadas, MD, Assistant Professor of Medicine, 2007 (mentoring on dataset building) • Savitri E. Fedson, MD, Assistant Professor of Medicine, UC, 2006-8 (microarray analyses)

Mentorship of Research Professors • Haiquan Li PhD, Res. Assoc. Prof., Dept. of Medicine, 2014-present, U of Arizona • Vincent Gardeux PhD, Res. Assist. Prof., Dept. of Medicine, 2014-present, U of Arizona • Haiquan Li PhD, Res. Assist. Prof., Dept. of Medicine, 2010-13 (U of C 2010-11, UIC 2011-13) • Younghee Lee, PhD, Res. Assoc (Assist. Prof.), Dept. of Medicine, 2010-2011 (K awarded in 2011) • Xinan Yang PhD, Res. Assoc (Assist. Prof.), Dept. of Medicine, 2010-2011 (planned K- award) • Andrew Boyd MD, Res. Assist. Prof., Dept. of Medicine, UIC, 2010-2012 (now tenure-track Assist Prof, UIC) • Yong Huang MD, Res. Assist. Prof., Dept. of Medicine, U of C, 2007-2011

Pre-Doctoral Research Advisor for • Grant Schissle, PhD candidate, 2014-present- Dept. Mathematics (Sect Bioinform.) Univ. of Arizona. • Qike Li, PhD candidate, 2014-present- Dept. Mathematics (Sect Bioinform.) Univ. of Arizona. • Peter LoPresti, MD/PhD candidate, 2012-13- Dept. Bioengineer. (Sect Bioinform.) Univ. of Ill. at Chicago. • Alan Perez-Rathke, MD/PhD candidate, 2012-13- Dept. Bioeng.(Sect Bioinform.) Univ. of Ill. at Chicago. • Gurunadh Parinandi, MSc, 2012-2013 Dept. Bioeng. (Sect Bioinform.) Univ. of Ill.at Chicago. • Kelly Regan, 2011-12 – Univ.of Chicago Honors Grad. (one year research staff, now MD/PhD candidate, College of Medicine at The Ohio State University) • Kanix Wang, 2011 – PhD candidate, University of Chicago- Committee on Genetics and Systems Biology. • Ying Tao, M.D., PhD (PhD completed in 2006 –Lussier main advisor). –Analyses and visualization of gene-phenotype relationship networks 2001-6, Columbia University. Dissertation: http://gradworks.umi.com/32/49/3249135.html

-Now: IBM Researcher https://researcher.ibm.com/researcher/view_pubs.php?person=cn-taoytao&t=1 • Matthew Crowson, 2008, Hamilton College student (summer research staff)- Now: Surgery Fellow, Duke Univ. • Sascha Goonewardena, MD, 2007-9, research rotation, Resident in Medicine • James Chen, BSc, MD candidate - Rotations (subintern) –Information theory & Phenotypic Ontologies, 2004

-Now: clinical & research fellow in hemato-oncology @ University of Chicago • Spiro P. Pantazatos, M.Sc., Ph.D. Candidate (rotation) – Cross-Scale Mapping of Gene Expression to Neuroimaging Datasets via Semantic Decomposition, Columbia University 2004-6 .

-Now: preparation of PhD dissertation @ Columbia University (Advisor: Joy Hirsch) • Lee Sam, M.A., Multistrategy Approaches to Retrieving Medical and Biological Evidence from Excerpts including Knowledge Extraction using Natural Language Processing, Ontologies-Anchored Classification and C and Case Base Reasoning of Evidence Based Medicine. 2004-6.

-Now: preparation of PhD dissertation @ University of Michigan (Advisor: Arul M. Chinnaiyan) • Michael Bales, Ph.D. Candidate, research rotation, 2005-9, Columbia Univ (PhD Committee),


• Tzu-Lin Hsiao, M.D., PhD (rotation) – Ontology-Anchored Phenomics & Anatomic, 2005, Columbia Univ • Chintan Patel, M.Sc., PhD (rotation) –Graph theory approaches to phenotypic integration, 2004, Columbia Univ • Paola Karina Tulipano, M.A., Ph.D. Candid., res. rotation, 2003-4, Columbia Univ- Now Scientist Philips labs. • Xiaoyan Wang, Ph.D., 2003-4, Columbia Univ.; Now: Assistant Professor @ University of Maryland • Neil Sarkar, Ph.D.(rotat., 2002-4) Columbia Univ.; Now: Assist. Prof. & Dir. Biomed. Inform., Univ. Vermont. • Jeeyai Choi, research rotation, Ph.D., 2002-3, Columbia University • Matthew A. Neimark, M.D. Ph.D. candidate (rotation) –Individualized Medicine, 2002, Columbia Univ • Chani Weinreb MD, (rotation)–Biomed. Database Interoperability, 2001, Columbia Univ

Post-Doctoral Fellowship Research Advisor for --Primary Advisor— • Nima Pouladi, MD/PhD, The University of Arizona (2014-present) • Ikbel Achour PhD, The University of Illinois at Chicago (2012-13), Now Res Assoc at The U of AZ • Vincent Gardeux PhD, The University of Illinois at Chicago (2012-13), and (ii) Assistant Professor in Computer Science at EISTI (Ecole Internationale des Sciences Traitement Information). Now Assist Prof at The U of AZ • James Chen MD, (i) Fellow, Hematology/oncology, The University of Chicago (2008-present), and (ii) Resident in Internal Medicine Georgetown University , Rotation, Univ. of Chicago 11-12/2006.

-Now: clinical & research hemato-oncology fellow @ Univ. of Chicago • Xinan Yang PhD, Post-Doctoral Fellow, computational analyses of microRNA expression and personalized expression profiling, The University of Chicago (2008-2010). - Now: RA Assistant Professor @ Univ. of Chicago • David Mann, MD, 2008-10, Resident in Dermatology, University of Chicago (research advisory role). • Younghee Lee, PhD, Post-Doct. 2007-10 Fellow, onco-microRNAs & genetics studies, Univ of Chicago

- Now: RA Assistant Professor @ Univ. of Chicago • Michael Cantor, M.D. M.Sc. (Post Doctoral fellowship) – Genomic Medicine, 2001-4, Columbia University

- Now: Dir. Of Biomed Inform @ Pfizer (Former Chief Medical Officer @ New York Univ, Bellevue Hospital) • Te-Hui Kuo, M.D., M.A. (Post-Doct. Fellow)–Mining Drug-Disease Contraindications, 2001-3, Columbia Univ • Hedi Hegyi, Ph.D., (Post-Doct.Fellow.), Columbia Univ., 2004-5; Now: Fellow, Inst.of Enzymology, Hungary --Secondary Advisor-- • Huiping Liu, PhD, Post-Doct. (Advisor: G Greene), 2010-2011(microRNA expression analyses). • Eun-Hee Shim, PhD, post-doct. (Advisor: J Cunningham laboratory), 2010-11 (genomic studies analyses). • Wei Zhang PhD, Fellow, Hematology/oncology, The University of Chicago (2009-10). • Tanguy Seiwert, MD (Microarray Analysis), Pulmonary Fellow, The University of Chicago, 2006-7. • Ankit Desai, cardiology fellow, MD (Microarray Analysis), Pulmonary Fellow, Univ of Chicago, 2006-7. • Chern-Sing Goh, Ph.D. (Post-Doctoral Fellowship) – Prokaryotic Phenome -2004-2005, Currently post-Doctoral Fellow at Gerstein Laboratory – Yale University. • Vincent Delbagno, M.D., M.A. (rotation) – Business Informatics, 2004, Columbia University • Aylit Schultz, MD, (subintern) – Clinical Phenotypes of Disease Genes, 2002-3, Columbia University

Master Degree and Undergraduate Research Advisor for • Edwin Walsh, B. Sc (engineering) 4th yr Pritzker School of Medicine Student, 2008. • James Deitzer, Bioengineer, M.A., 2005, Columbia Univ, Genomic Ontologies in SNOMED. • Tara Borlawsky, M.Sc. – Distributed Knowledge Management for Clinical Alerts, 2004, Columbia University.

-Now: Dir. Of Research Informatics Services, Ohio State University Ctr. • Daniel Rappaport, M.A. candidate, NLP & ontologies of genetic expression 2004-5, Columbia University. • Huinar Quek, M.A. – Biomed DB Interoperability, 2002-2003, Columbia Univ

-Now: Lecturer, Biomed Engineer., Nanyang Technol. Univ., Med Inform Dir, Ministry of Health (Singapore)

Academic advisor for • Pallav Sharda, M.A., 2002-3, Columbia Univ. – Now: Business Intelligence Lead, Kaiser Permanente. • Vincent M. Delbagno, M.D., M.Sc., 2002-4, Columbia University • Jianbo Lei, M.D.., M.Sc., 2002-2004, Columbia University.


• Kwok-Tim Chan, M.D., M.Sc., 2003-4, Columbia Univ-Now: Senior Med Officer, Dept. of Health, Hong Kong. • Sameer Malhotra, M.B.B.S., M.A., 2003-4, Columbia University.

Grants, Scholarship, Fellowship Support and Contracts Past Scholarships • 1986 Research Scholarship Graduate student, Fond de Recherche en Santé du Québec • 1987 Research Scholarship Graduate Student, Kidney Foundation of Canada • 1987 Research Scholarship Graduate Student, Fond de Recherche en Santé du Québec • 1998- 2001

Post-Doctoral Research Fellowship

Independent Research Fellowship – Medical Research Council of Canada (MRC) http://www.cihr-irsc.gc.ca/f/2798.html

Current Grants • 1S10RR029030-01 BEAGLE: A Supercomputer for Biomedical Simulation and Data Analysis Role/Period/$ Lead Investigator (among 12), Effort 5% (PI: I Foster) 2010 / $6,967,431 “Beagle” Cray XE6 Supercomputer of the Computation Institute: 150 Teraflop (17,856 cores; 1,488 processors;

23,3 terabyte of memory, 464 terabytes of disks drive). Lussier: modeling non-coding polymorphisms of health. • 3UL1RR024999-03S3 and NCI/CTEP, Multicenter randomized phase II study of Temsirolimus versus

Cetuximab +Temsirolimus in patients with recurrent/metastatic head and neck cancer CTSA-PI: J Solway; Trial Lead Investigators: Vokes E Lussier YA, Seiwert T; 2009/9-2011/8 / $282,714

Clinical hypothesis: the combination of mTOR inhibition (using temsirolimus) and EGFR inhibition (using cetuximab) prolongs progression free survival (PFS) in patients, who have failed EGFR based therapy, whereas mTOR inhibition alone does not provide a similar benefit. Underlying bioinformatically-initiated hypothesis: the combination of mTOR inhibition with temsirolimus and EGFR inhibition with cetuximab is synergistic in head and neck squamous cell carcinomas and overcomes primary and/or secondary resistance to cetuximab. Furthermore activity is driven by tumors with a myofibroblast (+) phenotype. • CA023074 Lussier (10%) NCI #CA023074Arizona Cancer Center Support Grant

Pending Grants – • 1R01CA190696-01 Schatz (PI) 9/1/14 – 8/31/19 0.60 calendar NIH/NCI $250,000 A New Treatment Paradigm for ALK-Driven Cancers Exploiting Oncogene Overdose This project will investigate gene-expression in lymphoma, using xenograft and transgenic mouse models, including a clinical component interfacing with a Novartis Oncology phase II trial currently underway. • U01 HL125208 Yuan/Rischard (MPI) 9/01/14 – 8/31/19 0.60 calendar (0.12 year 1) NIH/NHLBI $199,999 Phenomic and Genomic Study to Subphenotype Hispanics with Pulmonary Hypertension This grant will redefine pulmonary hypertension classification by employing a combination of physiological, genomic and epigenetic strategies to sub-phenotype Latino and non-Latino pulmonary hypertension patients across the 5 Groups of PH categories with the goal of enhancing our understanding of disease pathophysiology, progression and prognosis. • P01 HL 126609-01 Garcia (PI/PD) 02/01/2015 – 1/31/2020 1.2 calendar NIH/NHLBI $1,514,666 Cytoskeletal Regulation of Lung Endothelial Pathobiology Core B Leader This PPG, in its 16th-20th year of proposed funding, will integrate our deeply mechanistic, highly translational and clinically-relevant studies to drive new knowledge about the complex field of inflammatory lung injury. A major thematic direction is understanding the spatial regulation of the dynamic actomyosin cytoskeleton (central stress fibers, lamellipodia formation, focal adhesion formation) involving MLCK, cortactin, c-Abl, EVL, β-integrins. Furthermore, by utilizing functional genomics to evaluate ALI-associated SNPs (polymorphisms) for these key cytoskeletal-associated genes, our programmatic approaches are woven into experimental strategies that test novel therapies to attenuate inflammatory edema. This multi-faceted systems biology translational application will provide the basis of understanding for personalized therapies.


Completed Grants (3 categories) -Big Data Science, computational biology & biomolecular informatics • BEAGLE Supercomputer for Biomed. Sim. & Big Data Analysis (1S10RR029030-01; 2010-14; PI: I Foster, Lead Inv: Y Lussier; $7M; Cray XE6: 150 TFLOP; Cores:17,856; 1,488 processors; RAM: 23TB, disks: 464TB). • MAGNet Nat. Ctr the Multiscale Analysis of Genomic & Cellular Networks (5U54CA121852; 2005-2010; Role: Lead Inv. Natural Language Processing and Ontology, $400,000 of the $18,500,000) • Semantic Approaches to Phenotypic Databases Analyses (K22 LM008308 NLM, 5/2004-4/2008, $433,445) Role: PI, build innovative informatics tools capable of automatically querying and organizing phenotypic data. • Clinical-Genomics Knowledge-Bases for High Throughput Drug Discovery (NYSTAR Center for Advanced Technology Grant # C020054, PI, 2/2003-7/2003, $44,471) • Capturing and Linking genomic and clinical information (R01LM007659, 8/2003-9/2007, $1,400,000, role: co-PI). Use natural language processing (NLP) to facilitate cancer research by automatically extracting and organizing clinical and genetic information from the Electronic Medical Record (EMR) and from journal articles. • Intelligent Cooperative Communications for Cross-Organization and Real-Time Responsiveness (NYSTAR 2003-4 $43,140), PI, award winning collaboration with Rose Williams (IBM Watson Research Lab) to deploy secure and HIPAA compliant event-monitored communications over Smart Phones (VigiLENS). http://www.cat.columbia.edu/grant_recipients03.htm

-Translational clinical genomics & clinical informatics • Deranged Coagulation and Fibrinolytic Cascades in Idiopathic Pulmonary Fibrosis Role/Period/$ Lussier Co-inv., Effort - 2% 03/01/10-02/28/14 / $19,015 • 1U01HL105371 NIH/NHLBI Phase II study of inhaled Carbon Monoxide for treatment of IPF Role Lussier PI of the Subcontract (10%); (PIs: A Choi, JGN Garcia) 2010-3 $1,250,000/yr • 1R01CA142996-01 Genome-Wide Association Study of Breast Cancer in the African Diaspora? Role/Period/$ Co-investigator, Effort - 5% (PIs: NJ Cox, F Olopade) 2010-2014 / $1,250,000/yr • UL1RR029879 Ctr for Clinical & Transl. Science (University of Illinois at Chicago) Role/Period/$ Assoc. Dir. For Inform. (PIs: L Tobacman, R Mermelstein, L Tobacman) 2009-14 / ∼$17.5 M • Radiation response within the tumor microenvironment (PI: S. Kron) 1 R01 CA16449201 Role Co-investigator Total Project Period 2011-16 • VigiLENS Patient Health Monitoring (NASA VCU-528753/PO P417322, HRSA / Office of Advanced Telemedicine OAT, 2001-2002:$1,266,000, 2002-2003:$850,000, role: co-PI Lussier, PI: EH Shortliffe), An ontology-anchored and server accessible clinical event monitor for dramatically reduce the cost (TCO). • NIAID Northeast Research Center of Excellence for Biodefense and Emerging Infections Diseases (2003-2005 5U54 AI057158) Lead Investig, Bioinform Core Director, $59,872,920 ($5,117,861 to the Bioinform Core) • 1RC2HL101740-01 Molecular Markers of Idiopathic Pulmonary Fibrosis Progression Role Subcontract PI (Jointly with I Noth), Effort - 10% (PI: Martinez) 9/30/09-9/29/11 / $3,411,051 • 2 P01 CA040046-21, NCI Etiology of Alkylator-Induced Myeloid Leukemia Role/Period/$ Investigator in Project 1, Bioinform, Effort 5% (PI: M Le Beau) 9/2008-8/2011 / $2,100,525 • 5P50CA125183 SPORE on Breast Cancer Role/Period/$ Co-Investigator on Pilot Project (PI: OI “Funmi” Olopade) 2006-2011 / ∼$2,228,818/year • 5UL1RR024999 Clinical and Translational Science Awards (CTSA): University of Chicago Role/Period/$ Co-Dir., Biomed Inform. Core, Effort (PI: J Solway) 2007-11 / ∼$20,000,000 (∼1,500,000 BIC) • 5P30CA014599-35, NCI University of Chicago Comprehensive Cancer Center Support Grant Role/Period/$ Co-inv., Assoc. Dir. for Inform., (PI: M Le Beau) 9/2008-8/2011 / $4,368,460/year • T-AML:Harness Complex Science to Fight Cancer (Cancer Res. Found., 2008-11 $4.5M ($375k bionform.) • PAAR-U19GM061393-11 NCI/NIGMS Pharmacogenetics of Anticancer Agents research group Role/Period/$ Co-investigator, Effort - 5% (PIs: M Ratain, NJ Cox, E Dolan) 2010-2011 / ∼$12,500,000 • 1R01LM009725 NLM Enhancing organism based disease knowledge via taxonomic intelligence Role/Period/$ Co-investigator, Effort 5% (PI: IN Sarkar) 9/2008-8/2012 / $1,054,682


• Title Community Profile CTSA Supplement (PI: D. Hynes; Co-inv Lussier) RFA-CA-11-005; 2011-2 • Title CTSA/ Clinical Efficacy Research Supplement (PI: D. Meltzer, J. Krishnan;Lussier co-inv) 2011-2

-Basic Science of knowledge representation (e.g. ontologies) and natural language processing • Health Evidence and Application Linkages Network -HEALNet-RELAIS (Medical Research Council of Canada 1995-1998 $2,400,000; Role: Lead Inv, PIs: B Haynes&J Moehr), SNOMED in EMRs & directed graphs. • Unlocking data from medical records with text processing (R01LM06274 NLM, 1997-2000, $878,193, co-inv.) • Knowl Base of Clinical Traits for Human Dis Genes.NYSTAR Ctr Adv Techn #21240026, 2002-3, $19,000, PI • ICTVdb: The Universal Virus Information System (5G08LM007198-03, subcontract PI, 2004, $80,000). • Ontology-based Retrieval of Individualized Evidence-Base Excerpts (NYSTAR/CAT UPN: 04240001 5-67725 2005-6 $89,811 and John Wiley and Sons Publishers $200,000), PI. • A Biomedical Natural Language Processing Resource (1R01LM008635-01 NLM 2005-2009, $2,179,256) Co-Investigator (PI: C Friedman), Adapting natural processing system for use with SNOMED encoding. • ID/ Title 3UL1RR024999-03S5 Service Oriented Discovery Architecture: Semantic Expansion Project Role/Period/$ Adm. Suppl. Lead investigator- Effort 4% (PI: J Solway) 2009/9-2011/8 / $1,924,346 The key overall objective is to enable data integration from enterprise systems for translational researchers using SNOMED and UMLS – anchored clinical narratives (via natural language processing, as well as GRID-accessible ontology-server and NLP-server services). IRB Protocol 10-325-B .

Publications and Communications Journal Publications

1. Lussier A, Arseneault A, Varady A, De Médicis R, Lussier Y, Lebel E. "The use of a 51Cr Technique to Detect Gastrointestinal Microbleeding Associated with Nonsteroidal Anti-inflammatory Drugs". Semin Arthritis Rheum. 1988:17(3);40-45.

2. Lussier A, Davis A, Lussier Y. "Comparative Gastrointestinal Blood Loss Associated with Placebo, Aspirin and Nabumetone as Assessed by Radiochromium (51Cr)". J Clin Pharmacol 1989:29(3);225-228.

3. Lussier YA*: "Le Dossier Patient Informatisé sur ardoise électronique: le défi de Développement Purkinje". Canadian Medic Inform, 1994:1(1), 46-47.

4. Lussier YA*."Scientific Medicine in Need of a Standard Coded Nomenclature". Canadian Medic Inform 1994:1(4)

5 Lussier YA*, Côté RA: "Are We Closer to Standard Medical Coding?". Canadian Medic Inform 1995:2(5). 6 Lussier YA*, Rothwell DJ, Côté RA: "The SNOMED Model: A Knowledge Source for the Controlled

Terminology of the Computerized Patient Record". Methods Inf Med 1998:37;160-164. PMID: 9656658 7 Liu H, Lussier YA, Friedman C*. “Disambiguating Ambiguous Biomedical Terms in Biomedical Narrative Text:

An Unsupervised Method”. J Biom Inform 2001:34,249-261. ↳journal 8 Sarkar IN, Cantor MN, Gelman R, Hartel F, Lussier YA*. Linking biomedical language information and

knowledge resources: GO and UMLS. Pac Symp Biocomput., 2003;439-50.PMC1480054 ↳journal 9 Cantor MN, Sarkar IN, Gelman R, Hartel F, Bodenreider O, Lussier YA*. An evaluation of hybrid methods for

matching biomedical terminologies: mapping the gene ontology to the UMLS. Stud Health Technol Inform. 2003;95:62-7. ↳journal

10 Sarkar IN, Cantor MN, Gelman R, Hartel F, Lussier YA*. Linking biomedical language information and knowledge resources: GO and UMLS. Pac Symp Biocomput, 2003;439-50.PMC1480054 ↳journal

11 Lussier YA*, Li J. Terminological Mapping For High Throughput Comparative Biology of Phenotypes. Pac Symp Biocomp 2004;:202-13. ↳journal

12 Friedman C*, Shagina L, Lussier YA, Hripcsak G*. Automated Encoding of Clinical Documents Based on Natural Language Processing. J Am Med Inform Assoc 2004-11(5):392-402. PMC516246 ↳journal

13 Wang A, Quek HN, Cantor MN, Kra P, Schultz A, Lussier YA*. “Automating Terminological Networks to Link Heterogeneous Databases”. Stud Health Technol Inform. 2004;11(Pt 1):555-9. PMC2917348 ↳journal

14 Cantor MN, Lussier YA*. Mining OMIM for insight into complex diseases. Stud Health Technol Inform. 2004;107(Pt 2):753-7. PMC2883183


15 Tao Y, Friedman C, Lussier YA*. The Use of Information Visualization Techniques in Bioinformatics during the Postgenomic Era. Discov Today Biosilico. 2004; 2: 6. PMC2957900 ↳journal

16 Williams R*, Jalan S, Stern E, Lussier YA*. Cascading Policies Provide Fault Tolerance for Pervasive Clinical Communications. Proc of 3rd IEEE Internat Conf on Pervasive Computing and Communications Workshops, (PerComW), IEEE Computer Society 2005:209 – 212. ↳journal

17 Tao Y, Friedman C*, Lussier YA*. “Visualizing information across multidimensional post-genomic structured and textual databases” and textual databases” Bioinformatics. 2005 15;21(8):1659-67. ↳journal

18 Cantor MN, Sarkar IN, Bodenreider O, Lussier YA*. Genestrace: Phenomic Knowledge Discovery Via Structured Terminology. Pac Symp Biocomput. 2005;103-14. PMC2894422 ↳journal

19 Lussier YA*, Williams R, Jalan S, Borlawsky T, Li J, Stern E*. Partitioning Knowledge Bases Between Advanced Notification and Clinical Decision Support Systems. Decision Support Syst. 43(2007)1274-86↳journal

20 Zhou L, Tao Y, Cimino JJ, Chen ES, Lussier YA, Hripcsak G, Friedman C*. Terminology Model Discovery Using Natural Language Processing and Visualization Techniques. J Biomed Inform. 2006;39(6):626-36↳journal

21 Lussier YA*, Borlawsky T, Rappaport D, Friedman C*. PhenoGO: Assigning Phenotypic Context to Gene Ontology Annotations. Pac Symp Biocomput.,2006;:64-75. PMC2906243 ↳journal

22 Choi J, Bakken S*, Lussier YA*, Mendonca EA*. Improving the Human Readability of Arden Syntax Medical Logic Modules Using a Concept-oriented Terminology and Object-oriented Programming Expressions. Comput Inform Nurs. 2006 Jul-Aug; 24(4):220-5. ↳journal

23 Goh CS, Gianoulis TA, Liu Y, Li J, Paccanaro A, Lussier YA*, Gerstein M*. Integration of Curated Databases to Identify Genotype-Phenotype Associations. BMC Genomics 2006, 7:257. ↳journal • ↳Top-‐Paper “Bioinformatics Tool-Related Papers of Note”, October 2006, BioInform

24 Friedman C*, Borlawsky T, Xing HR, Lussier YA*. Bio-Ontology and Text: Bridging the Modeling Gap. Bioinformatics, 2006 Oct 1;22(19):2421-9. ↳journal

25 Liu Y, Li J, Sam L, Goh CS, Gerstein M*, Lussier YA*. An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PLoS Computational Biology, 2006 2(11): 1419-1435. ↳journal ★ Editor’s Pick of the month • ↳ISMB_2007-‐highlight, Selected as a highlight of 2007 for presentation in the Internat Symp on Mol Biol.

26 Tulipano KP, Tao Y, (…), Lussier YA*, Friedman C*. Natural Language Processing and Visualization in the Molecular Imaging Domain. J Biomed Inform, 40 2007; 270-281. ↳journal

27 Palacios G, (…), Lussier Y, Formenty P, Nichol MS, Feldmann H, Briese T, Lipkin WI*. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg Infect Dis. 2007 Jan;13(1):73-81. ↳journal

28 Lussier YA*, Liu Y. Computational Approaches to Phenotyping: High-Throughput Phenomics. Proc Am Thorac Soc Vol 4. pp 18-25, 2007. ↳journal

29 Tao Y, Li J, Friedman C, Lussier YA*. Information Theory Applied to the Sparse Gene Ontology Annotation Network to Predict Novel Gene Function. Bioinformatics, 2007, 23(13)i529-38.↳journal • ↳PRESS COVERAGE “Phenotype Lookup and Linkup: New Methods Arise to Mine Phenotypes for Gene

Function”, BioInform, Sept. 5, Vivien Marx. 30 Sam L, Li J, Liu Y, Friedman C, Lussier YA*. Discovery of Protein Interaction Networks Shared by Diseases. .

Pac Symp Biocomput, 12:76-87(2007). PMC2886192 ↳journal 31 Nonas SA, (…), Lussier YA, Garcia JG*. Use of Consomic Rats for Genomic Insights into Ventilator-Associated

Lung Injury. Am J Phys, Lung Cellular and Mol Physiol, 293: L292-L302, 2007 PMID:17468131 ↳journal 32 Bales M, Lussier YA*, Johnson SB*. Topological analysis of large-scale biomedical terminology structure. J

Am Med Inform Assoc. 2007 Nov–Dec; 14(6): 788–797. ↳journal 33 Jabado OJ, Liu Y, Conlan S, Quan PL, Hegyi H, Lussier Y, Briese T, Palacios G, Lipkin WI*. Comprehensive

viral oligonucleotide probe design using conserved protein regions. Nucleic Acids Res. 2008;36(1):e3. ↳journal

* Corresponding author(s) § These authors have contributed equally to the work.


34 Moreno-Vinasco L, (…), Lussier YA, Garcia JGN*. Genomic Assessment of a Multikinase Inhibitor, Sorafenib, in a Rodent Model of Pulmonary Hypertension. Physiol Genomics 2008, 33: 278–291. PMID:18303084 ↳ journal

35 Hong SB, Huang (…), Lussier YA, Garcia JGN*. Essential Role of Pre-B Cell Colony Enhancing Factor in Ventilator-Induced Lung Injury. Am J Respir Crit Care Med, 2008 Sep 15;178(6):605-17. PMC2542434 ↳journal

36 Wang T, Moreno-Vinasco L, Huang Y, (…), Lussier YA, Natarajan V, Garcia JGN*. Murine Lung Responses to Ambient Baltimore Particulate Matter: Genomic Analysis and Contribution to Airway Hyperresponsiveness. Environ Health Perspect. 2008;116(11):1500-8. PMC2592270 ↳journal

37 Liu Y, Sam L, Li J, Lussier YA*. Robust Methods for Accurate Diagnosis Using Pan-Microbiological Oligonucleotide Microarrays. BMC Bioinformatics 2009 5;10,2:S11.↳journal • ↳AMIA-2008-award; Outstanding Paper Award, American Med Inform Assoc • ↳PRESS COVERAGE “Progress in linking clinical and biomedical informatics” BioInform, 3/20/09 Vivien Marx.

38 Sam L. Li J, Mendonca E, Blake J, Friedman C, Lussier YA*. PhenoGO: A Resource for Mining Multiscale Biological and Clinical Data. BMC Bioinformatics. 2009 Feb 5;10, 2:S8. ↳journal • ↳AMIA-2008-award; Outstanding Paper Award, American Med Inform Assoc

39 Pantazatos SP, Li J, Pavlidis P, Lussier YA*. Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. Cancer Informatics, 2009:8 75–94. PMC2874327 ↳journal

6th most highly visible since 2009 (>5900 articles views) 40 Meyer NJ, Huang Y, Singleton PA, Sammani S, Moitra J, Evenoski CL, Husain AN, Mitra S, Moreno-Vinasco L,

Jacobson JR, Lussier YA, Garcia JGN*. GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling. FASEB J. 2009 May;23(5):1325-37. ↳journal

41 Yang X, Huang Y, Chen J, Xie J, Sun X, Lussier YA*. Mechanism-Anchored Profiling derived from Epigenetic Networks Predicts Outcome in Acute Lymphoblastic Leukemia. BMC Bioinformatics 2009, 10(Suppl 9):S6 PMC2745693 ↳journal • ↳AMIA-2009-award ; Outstanding Paper Award, American Med Inform Assoc

42 Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Youngfei Wu, Li J, Hasina R, Cheng C , Lingen MW, Gerstein M, Weichselbaum RR, Xing HR*, Lussier YA* (2010) Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis. PLoS Comput Biol 6(4):e1000730. PMC2848541 ↳ journal ★ One of the 24 best translational bioinformatics reports of 2009-10, REVIEW by Russ Altman, presented at

the 2010 American Medical Informatics Association Summit on Translational Bioinformatics and on his blog http://rbaltman.wordpress.com/ (page 36 of the PDF file, URL below): ↳Presentation ; ↳AMIA-‐Highlight-‐of-‐the-‐year-‐2010

• ↳AMIA -‐2010-‐late-‐breaking-‐news; Selected as late breaking news (5 selected) for highlight in The 2010 Am Med Inform Assoc Summit on Translational Bioinformatics; S12, p.17

• ↳ ISMB_2011-‐highlight_of_the_year; Selected as a highlight of 2011; Internat Symp on Mol Biol. • ↳PRESS COVERAGE “Streamlining the Language of Genetic Medicine” by Robert Mitchum, Focus, 10/19/2009

43 Chen J§, Sam L§, Huang Y§, Lee Y, Li J, Liu Y, Xing HR, Lussier YA*. Protein Interaction Network Underpins Concordant Prognosis Among Heterogeneous Breast Cancer Signatures. J Biomed Inform, ;43(3):385-96 2010 Mar 27. PMC2878851 ↳journal

44 Yang X§, Huang Y§, Crowson M, Li J, Maitland M*, Lussier YA*. Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data. J Biomed Inform. 43 (2010) 376–384. PMC2893391 ↳journal

45 Yang X, Lee Y, Fan H, Sun X*, Lussier YA*. Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancer. Chinese Sci Bull, 2010, 55, No.31: 3576-3589. PMC3039912 ↳journal

46 Yang X§, Lee Y§, Huang Y, Chen J, Xing HR* , Lussier YA*. Stromal Microenvironment Processes Unveiled by Biological Component Analysis of Gene Expression in Xenograft Tumor Models. BMC Bioinformatics 2010, 11(Suppl 9):S11doi:10.1186/1471-2105-11-S9-S11. PMC2967741 ↳journal. • ↳AMIA-2010-award; Outstanding Paper Award from the Am Medic Inform Assoc. “Selected for

publication in BMC Bioinform to recognize twelve exceptional 2010 TBI Summit papers.” 47 Gamazon ER, Im HK, Lussier YA, Cox NJ, Dolan ME, Zhang W*. ExprTarget: An integrative approach to

predicting human microRNA targets. PLoS One, 2010 Oct 21;5(10):e13534. PMC2958831. ↳journal 48 Mirzapoiazova T, (…), Lussier YA, Watterson MD, Dudek SD, Garcia JGN*. The Non Muscle Myosin Light

Chain Kinase Isoform is a Viable Molecular Target in Acute Inflammatory Lung Injury. Am J Respir Cell Mol Biol. 2011 Jan;44(1):40-52 PMC3028257 ↳journal


49 Mathew B, Jacobson JR, Huang Y, (…), Dudek SM, Natarajan V, Lussier YA, Weichselbaum RR*, Garcia JGN*. Simvastatin Attenuates Radiation-Induced Murine Lung Injury and Dysregulated Lung Gene Expression. Am J Respir Cell Mol Biol 2011 Mar;44(3):415-22. PMC3095940↳journal

50 Godley LA, Cunningham J, Dolan ME, Huang RS, Gurbuxani S, McNerney ME, Larson RA, Leong H, Lussier Y, Onel K, Odenike O, Stock W, White KP, Le Beau MM*. An integrated genomic approach to the assessment and treatment of acute myeloid leukemia. Semin Oncol. 2011;38(2):215-24. PMID:21421111 ↳journal

51 Yang X, Lee Y, Li J, Lussier YA*. GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. Bioinformatics 2011 May 15;27(10):1444-6. PMC3087953 ↳journal • Web service http://lussierlab.org/GO-‐Module

52 Sammani S,(…),Lussier YA, (…),Garcia JGN*. A Sphingosine 1-Phosphate 1 Receptor Agonist Modulates Brain Death-Induced Neurogenic Pulmonary Injury. Am J Respir Cell Mol Biol. 2011;45(5):1022-7.PMC3262681 ↳journal

53 Mathew B, Jacobson JR, Berdyshev E, Huang Y, (…), Lussier YA, Dudek SM, Natarajan V, Weichselbaum RR, Garcia JG*. Role of sphingolipids in murine radiation-induced lung injury: protection by sphingosine 1-phosphate analogs. FASEB J. 2011;25(10):3388-400. PMC3177585 ↳journal

54 Patwa LG, (…), Lussier YA, R. Sartor RB, Hansen JJ*. Chronic intestinal inflammation induces stress response genes in commensal Escherichia coli. Gastroenterology. 2011;141(5):1842-1851.e10. PMID 21726510 ↳journal

55 Chen J, Li J, Huang Y, Stadler W, Lussier YA*. Protein-Network Modeling of Prostate Cancer Gene Signatures Reveals Essential Pathways in Disease Recurrence. J Am Med Inform Assoc2011;18:392-402↳journal PMC3128407 ★ Editor’s pick of the month

56 Wang T, Lang G, Moreno-Vinasco L, Huang Y, (…), Lussier YA, Dudley S, Prabhakar N, Garcia JGN*. Particulate Matter Induces Cardiac Arrhythmias in Mice with Heart Failure via Dysregulation of Carotid Body Sensitivity and Cardiac Sodium Channels. Am J Respir Cell Mol Biol. 2012;46(4):524-31 PMID:22108299 ↳journal

57 Lussier YA*, Salama JK, Khodarev N, Xing HR, Huang Y, Hasselle MD, Zhang Q, Malik E, Darga TE, Fan H, Perakis A, Filippo M, Yang X, Lee Y, Chmura SJ, Hellman S, Weichselbaum RR*. MicroRNA expression characterizes oligometastasis(es). PLoS ONE 2011,6(12):e28650. ↳journal PMC3236765 * Corresponding authrors

58 Li Z, (…), Lussier YA, Zhang Y, Larson RA, Le Beau MM, Caligiuri MA, Bullinger L, Valk PJM, Delwel R, Loewenberg B, Liu PP, Marcucci G, Bloomfield CD, Rowley JD, Chen J*. Up-regulation of a HOXA-PBX3 homeobox-gene signature following down-regulation of miR-181 is associated with adverse prognosis in patients with cytogenetically-abnormal AML. Blood, 2012 Mar 8;119(10):2314-24. PMC3311258 ↳journal

59 Ferreira C, Chen JL, Li J, Shimomura K, Yang X, Lussier YA*, Pinto LH*, Solway J*. Genetic interactions between loci on chromosomes 11 and 18 contribute to native airway constrictor hyperresponsiveness in A/J vs C57Bl/6 mice. PLoS One. 2012;7(1):e29579. PMC3254621 *Corresponding authors ↳journal

60 Grassi MA, (…), Lussier YA, Cox NJ, Nicolae DL*. Replication Analysis for Severe Diabetic Retinopathy. Invest Ophthalmol Vis Sci. 2012;53(4):2377-81. ↳journal PMID: 22427569

61 Li H, Lee Y, Li J, Chen JL, Rebman E, Lussier YA*. Complex-Disease Networks of Trait-Associated SNPs Unveiled by Information Theory. J Am Med Inform Assoc 2012;19:295-305 PMC3277620 ↳journal • ↳AMIA-2011-award; Distinguished paper, Am Med Inform Assoc, ↳AMIA 2011 announcement ; ★ One of the 24 best translational bioinformatics reports of 2012, by Russ Altman, in his review presented at

the 2012 American Medical Informatics Association Summit on Translational Bioinformatics and on his blog http://rbaltman.wordpress.com/ ↳AMIA_Highlight-‐of-‐the-‐year-‐2012;

62 Regan K, Wang K, Doughty E, Li H, Li J, Lee Y, Kann M*, Lussier YA*. Translating Mendelian and complex inheritance of Alzheimer's disease genes for predicting unique personal genome variants. J Am Med Inform Assoc 2012;19:306-316 PMC3277633 ↳journal . • Provisional patent application.

63 Chen JL, Li J, Kiriluk K, Rosen A, Paner G, Antic T, Lussier YA, Vander Griend DJ*. Deregulation of a Hox Protein Regulatory Network Spanning Prostate Cancer Initiation and Progression. Clin Cancer Res. 2012 Aug 15;18(16):4291-302. Epub 2012 Jun 21. PMC3479663 ↳journal

64 Yang X, Regan K, Huang Y, Li J, Seiwert TY, Cohen EEW, HR Xing, Lussier YA*. Single Sample Expression-Anchored Profiles of Oncogenic Mechanisms Predict Survival in Head and Neck Cancer. PLoS Comput Biol 2012;8(1): e1002350. ↳journal PMC3266878 PLoS Comput Biol. 2014 ↳Correction PMID:24785253 • Late breaking news of the ISMB 2012 (Internat Symp on Mol Biol.) • ↳ ISMB_2013-‐highlight_of_the-‐year; Selected as a highlight of 2013; Internat Symp on Mol Biol.


65 Lee Y, Gamazon ER, Rebman E, Lee Y, Lee S, Dolan ME, Cox NJ*, Lussier YA*. Variants Affecting Exon Skipping Contribute to Complex Traits. PLoS Genetics 2012 8(10):e1002998. ↳journal • Best in Show, 2012 Dept of Medicine Res. Day, Un. of Chicago ↳DOM-‐Awards-‐2012

66 Chen J, Hsu A, Yang X, Li J, Parinandi G, Lussier YA*. Curation-Free Biomodules Mechanisms in Prostate Cancer Predict Recurrent Disease. BMC Genomics 2013, 6(Suppl 2):S4 ↳journal

67 Lussier YA*, Regan K, Khodarev NN, Corbin K, Li H, Khan SA, Ganai S, Gnerlich J, Darga TE, Fan H, Huang Y, Karpenko O, Posner MC, Chmura SJ, Hellman S, Ferguson MK, Weichselbaum RR. MicroRNAs of oligometastasis(es) progression predict survival better than initial metastatic presentation. PLoS One, 7(12): e50141. ↳journal

68 Payne PRO, Pressler TR, Sarkar IN, Lussier YA*. People, organizational, and leadership factors impacting informatics support for clinical and translational research. BMC Medical Informatics and Decision Making 2013, 13:20 ↳journal PMC3577661

69 Lee Y, Li H, Li J, Rebman E, Regan KE, Gamazon ER, Chen JL, Yang X, Cox NJ, Lussier YA*. Network Models of GWAS Uncover the Topological Centrality of Protein Interactions in Complex Disease Traits. J Am Med Inform Assoc 2013 Jul 1;20(4):619-29. PMID:23355459 ↳journal • Late breaking news of the AMIA Summit on Translational Bioinformatics 2013 • ↳Best-‐TBC-‐2012-‐paper-‐award; Translational Bioinformatics Conference 2013 • Highlighted in Editorial “Making it personal: translational bioinformatics”. AJ Butte, L Ohno-Machado. J

Am Med Inform Assoc 2013;20:4 595-596. 70 Perez-Rathke A, Li H, Lussier YA*. Interpreting Personal Transcriptomes: Personalized Mechanism-scale

profiling of RNA-Seq Data. Pacific Symposium in Biocomputing 18:159-170(2013). PMC3595401 ↳journal • “Sequencing paper of note” Genomeweb (3/5/2013): ↳reference

71 Boyd A, Burton MD, Li J, Jonen M, Gardeux V, Achour I, Bahroos N, Zenku I, Brown SB, Vanden Hoek T, Lussier YA*. The discriminatory cost of ICD-10-CM transition between clinical specialties: metrics, case study and mitigating tools. J Am Med Inform Assoc 2013 Jul-Aug;20:708-717 ↳journal PMID: 23645552

3rd most accessed JAMIA paper (Jul 2013 – June 2014) ; “5th Top Topic Aug 2013- June 2014” • Cited in >4,380 web pages (ICD10 + convoluted + University of Illinois; May 9 2013) • 150 to 400 users/day on the web conversion tool: http://lussierlab.org/transition-‐to-‐ICD10CM • Top ten downloaded for 14 consecutive months.

72 Herazo-Maya JD, Noth I, Richards TJ, Ma SF, Juan-Guardela BM, Tseng GC, Lussier YA, Huang Y, Vij R, Lindell KO, Gibson KF, Shapiro SD, Duncan SR, Garcia JGN*, Kaminski N*. Identification and Characterization of a peripheral Blood Mononuclear Cell Gene Expression Signature Predictive of Survival in Patients with Idiopathic Pulmonary Fibrosis. Sci Transl Med 2013 Oct 2;5(205):205ra136. PMID:24089408 ↳journal

73 NK Venepalli1, Y Qamruzzaman, J Li, YA Lussier, Andrew D. Boyd*. Identifying Clinically Disruptive ICD-10-CM Conversions to Mitigate Financial Costs Using an Online Tool. J Oncology Practice 2014 Mar 1;10(2):97-103. ↳journal PMID:24520143

74 Huang LS, Mathew B, Li H, Zhao Y, Ma SF, Noth I, Reddy SP, Harijith A, Usatyuk PV, Berdyshev EV, Kaminski N, Zhou T, Zhang W, Zhang Y, Rehman J, Kotha SR, Gurney TO, Parinandi NL, Lussier YA, Garcia JG, Natarajan V. The Mitochondrial Cardiolipin Remodeling Enzyme Lysocardiolipin Acyltransferase (LYCAT) is a Novel Target in Pulmonary Fibrosis. Am J Respir Crit Care Med. 2014 Jun 1;189(11):1402-15PMID:24779708 ↳journal

75 Maienschein-Cline M, Lei Z, Gardeux V, Bahroos N, Lussier YA.* ARTS: Automated Randomization of Multiple Traits for Study Design. Bioinformatics 2014 2014 Jun 1;30(11):1637-9 PMC4029038 ↳journal

76 Gardeux V, Arslan AD, Achour I, Ho TT, Beck WT*, Lussier YA*. Concordance of deregulated mechanisms unveiled by N-of-1-pathways in underpowered experiments: PTBP1 knockdown case study. BMC Genomic Medicine 2014, 7(Suppl 1):S1 ↳journal

77 Yang X, Huang Y, Lee Y, Gardeux V, Achour I, Regan K, Rebman E, Li H, Lussier YA*. In Silico Cancer Cell versus Stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment. BMC Genomic Medicine 2014, 7(Suppl 1):S2 ↳journal ↳supplements


78 Caskey R, Zaman J, Nam H, Chae SR, Williams L, Mathew G, Burton M, Li J, Lussier YA, Boyd AD. The Transition to ICD-10-CM: Potential Challenges for Pediatric Practice. Pediatrics 2014 Jul;134(1):31-6. PMID:24918217 ↳journal • ↳Editorial Fiks AG, Grundmeier RW. Elucidating Challenges and Opportunities in the Transition to ICD-

10-CM. Pediatrics. Online June 2, 2014. 80 Wang AL, Rao V, Chen J, Lussier Y, Rehman J, Huang Y, Jager R, Grassi M. Role of FAM18B in diabetic

retinopathy. Molecular Vision 2014; 20:1146-1159. ↳journal 81 AD Boyd, YM Yang, J Li, Kenost C, Burton MD, Bryan Becker, Lussier YA, Challenges and remediation for

Patient Safety Indicators in the transition to ICD-10-CM. (in press 5/2014), J Am Med Inform Assoc. 82 Gardeux V, Achour I, Maienschein-Cline M, Parinandi G, Pesce L, Li J, Li H, Foster I, Garcia JGN, Lussier

YA*. N-of-1-pathways” unveils personal deregulated mechanisms from a single pair of RNA-seq samples: towards precision medicine. J Am Med Inform Assoc 2014 online 6/12. ↳journal • ↳Best-‐TBC-‐2013-‐paper-‐award; Translational Bioinformatics Conference 2013

83 AD Boyd*, Li J, Kenost C, Joese B, YM Yang, OA Kalagidis, J Li, Zenku I, Saner D, Bahroos N, Lussier YA*. Metrics and mitigating tools after the transition to ICD-10-CM. J Am Med Inform Assoc 2014 minor revisions.

----------- Manuscripts under consideration ---------------- - Winn R, Bikkavilli RK, Avasarala S, Scoyk MV, Arcaroli J, Bezezinsky C, Zhang W, Edwards M, Kumar M, RathinamK, Zhou T, Tauler J, Borowicz S, Lussier YA, Parr B, and Cool C. Wnt7a is a novel inducer of β-catenin-independent Tumor-Suppressive Cellular Senescence in Lung Cancer. AACR Discovery Research Journal. -Krive J, Li JJ, Satava RA, Lussier YA*, Boyd AD*, “ICD-10 procedures produces discriminatory billing challenges between surgical specialties”. Journal of the American College of Surgeons. - Amin AD, Rajan SS, Lang WS, Pongtornpipat P, Groysman MJ, Tula-Sánchez AA, Peters TL, Cuyugan L, Rimsza LM, Lussier YA, Puvvada SD, Schatz JH. Drug-Induced Over-Expression of NPM-ALK Permits Therapeutic Exploitation of Oncogene Overdose. Science Translational Medicine. ----------- Manuscripts in Preparation ----------------- - Abraham I, AD Boyd*, Predicting COPD rehospitlizations using network-derived comorbidities. -Li H, Achour I, Gardeux V, Pesce L, Moore J, Foster I, Lussier YA. The regulatory (concordant?) interactions between non-protein coding and intragenic polymorphisms in complex diseases. In prep. for Nature Genetics -Li H, Achour I, Gardeux V, Pesce L, Moore J, Foster I, Lussier YA. Novel diseases syndromes in clinical records share common genetic mechanisms. In prep. for Nature Genetics -Huang Y, Zhang Q, Yang X, Lee Y, Fan H, Cohen K, Lussier YA. Stromal signature of rapamycin-induced vascular destruction predicts clinical outcome in breast cancer. In preparation - Wang S, Lussier YA. Bioinformatically-initiated clinical trials review. - Boyd, Lussier. ICD-10-CM oma for JAMA - Abraham Lussier. ICD-10-CM in California or UHC impact for JAMA - Lussier YA, Ram S. Netowrks & health care big data. - Gardeux, Qike, Nima, n-of-1-pathways simulation. Perhaps two papers, one for the vector and one for he biostatistics. - Achour I, Lussier YA, (Ideker, Califano, Butte??? Moore, ) review of dioseases & computations on encode. Nature Genetics - Achour I, Lussier YA, (Ideker, Califano, Butte??? Moore, ) review of precision medicine & bioinformatics. Nature Genetics or NEJM or JAMA? - ITS and predictions in medicine. Haiquan Lussier review


Refereed Conference Papers 84 Lussier YA*; Maksud M; Yale PP; St-Arneault R: "PureMD: A Computerized Patient Record Software for Direct

Data Entry by Physicians Using a Keyboardless Pen-Based Portable Computer". 16th Ann Sympon Comp Appl in Medl Care SCAMC 92; AMIA McGraw-Hill 1992,261-264. PMC2248094 ↳journal ★ ↳OCTAS-‐1994-‐award; Description of Dossier: Purkinje.com’s Award-winning pen-computing EMR anchored

on a terminology of 65,000 clinical concepts organized as a directed acyclic graph. “Octas of Excellence”. • Purkinje.com’s EMR used in ~2000 clinics and hospitals (renamed “Dossier” rather than PureMD).

85 Grant AM*; Lussier YA; Délisle E; Dubois S; Bernier R: "The TEAM Evaluation Approach to Project FAMUS". SCAMC 92, AMIA McGraw-Hill 1992, pp.734-738. PMC2248005 ↳journal

86 Lussier YA*; Bourque M: “Comparing SNOMED and ICPC Retrieval Accuracies Using Relational Database Models”. Proc AMIA 1997 Annu Fall Symp. 514-8. PMC2233545 ↳journal

87 Spackman KA*, Lussier YA, Campbell KE. Implementing SNOMED in Clinical Databases and Applications. Journal of Health Information Management. Ann Healthcare Inform & Managmt Systems Soc. HIMSS 1998 4p.

88 Kukafka R§, Lussier YA§, Cimino JJ: “Modeling Patient Response to Acute Myocardial Infarction: Implications for a Tailored Technology-Based Program to Reduce Patient Delay”. AMIA 1999 Proc Annu Fall Symp:570-4. PMC2232851 ↳journal

89 Lussier YA*, Kukafka R, Patel VL, Cimino JJ: “Formal Combinations of Guidelines: A Requirement for Self-Administered Personalized Health Education”. Proc. AMIA 2000:522-6. PMC2243904 ↳journal

90 Lussier YA, Shagina L, Friedman C. Automating SNOMED coding using medical language understanding: a feasibility study. Proc AMIA 2001 Annu Fall Symp.;:418-22. PMC2243482 ↳journal

91 Liu H, Lussier YA, Friedman C. A study of abbreviations in the UMLS. AMIA 2001 Proc Ann Fall Symp. 393-7. PMC2243414 ↳journal

92 Kukafka R§, Lussier YA§, Patel VL, Cimino J. 2001. Developing Tailored Theory-Based Educational Content for WEB Applications: Illustrations from the MI-HEART Project. Medinfo 2001. 10(2):1474-8. PMC2883864 ↳journal

93 Kukafka R§, Lussier YA§, Patel VL, Cimino JJ. Web-Based Tailoring and its Effect on Self-Efficacy. Results of the MI-HEART Randomized Controlled Trial. AMIA 2002 Proc Annu Fall Symp. 410-4. PMC2244518 8

94 Cantor MN, Lussier YA*, A knowledge framework for computational molecular-disease relationships in cancer. Proc AMIA 2002 Annu Fall Symp. 101-5. PMC2244393 ↳journal

95 Tao Y, Wang D, Shortliffe EH, Lussier YA*. Extended Attributes of Event Monitor Systems for Criteria-Based Notification Modalities. Proc AMIA 2002 Annu Fall Symp:762-6. PMC2244499 ↳journal

96 Lussier YA*, Sarkar IN, Cantor MN. An Integrative Model for In-Silico Clinical-Genomics Discovery Science. Proc AMIA Annu Fall Symp. 2002;:469-73. PMC2244185 ↳journal

97 Cantor MN, Lussier YA*. Putting Data Integration into Practice: Using Biomedical Terminologies to Add Structure to Existing Data Sources. Proc AMIA 2003 Annu Symp Proc.125-9. PMC1480054 ↳journal

98 Tao Y, Mendonca EA, Lussier YA*. “A tool for Abstracting Relevant Classes of Concepts: the Common Ances-try Summarizer”. Medinfo 2004;11(Pt1):449-53.PMC2879046 ↳journal

99 Cantor MN, Lussier YA*. “Mining OMIM for Insight in Complex Diseases”. Medinfo 2004;11(Pt 2):753-7. PMC2883183 ↳journal

100 Borlawsky T, Friedman C, Lussier YA*. Generating Executable Knowledge for Evidence-Based Medicine Using Natural Language and Semantic Processing. Proc AMIA 2006 Annu Symp Proc. 56-60. PMC1839756 ↳journal

101 Pantazatos SP; Li J; Pavlidis P; van Horn JD, Lussier YA*. Cross-Scale Mapping of Gene Expression to Neuroimaging Datasets via Semantic Decomposition. Medinfo 2007: Proc of the 12th World Congress on Health Inform; Building Sustainable Health Syst; [2282-4]. Kuhn, KA (Editor); Warren, JR (Editor); Leong, TY (Editor). Amsterdam: IOS Press, 2007. Studies in health technology and informatics, ISSN 0926-9630 .

102 Chen ES, Stetson PD, Lussier YA, Markatou M, Hripcsak G, Friedman C. Detection of Practice Pattern Trends through Natural Language Processing of Clinical Narratives and Biomedical Literature. AMIA 2007 Annu Symp Proc. 120-4. PMC2655911 ↳journal

103 Tao Y, Patel C, Friedman C, Lussier YA*. PIE: A Phenotype Interface Engine for Automated Representation in PATO and “Semantic Web”-Based Exchange of Clinical Data and Narratives. AMIA 2007 Annu Symp Proc. 645- PCM18693915 ↳journal

104 Lee Y, Li J, Gamazon E, Tikhomirov A, Cox NJ*, Lussier YA*. Biomolecular Systems of Disease Buried Across Multiple GWAS Unveiled by Information Theory and Ontology. AMIA 2010 Summits Transl Sci Proc. 31-35 PMC3041547 ↳journal * corresponding authors


105 Borlawsky TB, Li J, Friedman C*, Lussier YA*, Evaluation of an Ontology-anchored Natural Language-based Approach for Asserting Multi-scale Biomolecular Networks for Systems Medicine. AMIA 2010 Summits Transl Sci Proc.,6-10. PMC3041541 ↳journal * corresponding authors

106 Chard K, Russell M, Lussier YA*, Mendonça EA* Silverstein JC*. A Cloud-based Approach to Medical NLP. AMIA 2011 Annu Symp Proc:207-16. PMC3243210 *corresponding authors ↳journal

107 Chard K, Russell M, Lussier YA*, Mendonça EA* Silverstein JC*. Scalability and Cost of a Cloud-based Approach to Medical NLP. 24th IEEE 2011 CBMS Internat Symp on Computer-Based Medical Systems 24th; 1-6 ↳journal * corresponding authors

108 Yang X, Li H, Regan K, Li J, Huang Y, Xing HR, Lussier YA*. Towards Mechanism Classifiers: Expression-anchored Gene Ontology Signature Predicts Clinical Outcome in Lung Adenocarcinoma Patients. AMIA 2012 Annu Symp Proc. 1040-9. PMC3540430 ↳journal

109 Embi PJ, Tachinardi U, Lussier Y, Starren J, Silverstein J. Integrating Governance of Research Informatics and Health Care IT Across an Enterprise: Experiences from the Trenches. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:60-2. eCollection 2013.

110 Di Eugenio B, Boyd A, Lugaresi C, Balasubramanian A, Keenan GM, Burton M, Rezende Macieira TG, Dunn Lopez K, Friedman C, Li J, Lussier YA. PatientNarr: Towards generating patient-centric summaries of hospital stays. 8th International Natural Language Generation Conference (INLG). Proceedings.

111 Lee YJ, Boyd AD, Li J, Gardeux V, Kenost C, Saner D, Li H, Krishnan JA*, Lussier YA*. COPD Hospitalization Risk Increased with Distinct Patterns of Multiple Systems Comorbidities Unveiled by Network Modeling. AMIA 2014 Annu Symp Proc. In press

Original knowledge bases 112 Côté RA*; Lussier YA*: "Glossary of signs and symptoms". American College of Pathology, Secretariat of the

Systematized Nomenclature of Veterinary and Human Medicine. SNOMED vers 3.2, (CD), 1995, 1998. ↳journal

Editorial and Perspectives 113 Stevens R*, Bodenreider O*, Lussier YA*.Semantic webs for life sciences.Pac Symp Biocomput. 2006;112-5.↳J 114 Lussier YA*, Younghee Lee Y, Radivojac P, Ofran Y, Punta M, Butte A, Kann M; Session Intro. Molecular

Bioinformatics for Diseases: Protein Interactions and Phenomics.Pac Symp Biocomp 2008 1413:228-30 ↳journal 115 Lussier YA, Lee Y, Radivojac P, Ofran Y, Butte A, and Kann M. Molecular Bioinformatics for Disease - Session

Introduction. Pac Symp Biocomp 14:464-466(2009) ↳journal 116 Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O. Selected proceedings of the First Summit on

Translational Bioinformatics 2008 (Editorial). BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:I1. doi:10.1186/1471-2105-10-S2-I1. PMC2646246 ↳journal

117 Lussier Y, Butte A, Hunter L. Special Issue on Methodologies for Translational Bioinformatics (Editorial). Journal of Biomedical Informatics, 42 (2009) 201-2. PMC2894568 ↳journal

118 Lussier Y, Sarkar IN. Selected proceedings of the 2009 Summit on Translational Bioinformatics (Editorial). BMC Bioinformatics 2009, 10 (Suppl 9):I1. PMC2745679 ↳journal

119 Lussier YA*, Butte AJ, Hunter L. Current Methodologies for Translational Bioinformatics. Journal of Biomedical Informatics (Editorial). 2010 Jun;43(3):355-7. PMC2894568. ↳journal

120 Neil Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L*. Translational bioinformatics: linking knowledge across boil. and clinic realms. J Am Med Inform Assoc 2011;18(4):354-7. PMC3128415 ↳journal

121 Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Translational Bioinformatics: A Macroscopic Approach to Bridge the Biological and Clinical Divide. J Am Med Inform Assoc. 2011; 18(4):354–7. PMC3128415 ↳journal

122 Lussier YA, Chen JL. The Emergence of Genome-Based Drug Repositioning (Editorial). Science Translational Medicine 2011 Aug 17;3(96):96ps35. PMID:21849663 ↳journal • ↳Wall Street Journal “Researchers Show Gains in Finding Reusable Drugs”,9/18/2010.Amy Dockser

Marcus. • ↳ in GenomeWeb “Studies Describe Expression-based Strategy for Finding New Uses for Existing Drugs”.

Genomeweb Daily News, 8/17/2011. • ↳ in iHealthBeat “Computer Analysis Could Find New Uses for Existing Drugs”, iHealthBeat, 8/18/2011.

123 Lussier YA, Li H. Breakthrough in genomics data fusion for predicting clinical outcome. J Biomed Inform.2011;45(6):1199-1201. ↳journal


Scientific Reviews 124 Lussier YA*, Liu Y. Computational Approaches to Phenotyping: High-Throughput Phenomics. Proc Am Thorac

Soc 2007(4)18-25 ↳journal 125 Lussier YA*, Stadler WM, Chen JL. Advantages of Genomic Complexity: Bioinformatics Opportunities in

MicroRNA Cancer Signatures. J Am Med Inform Assoc 2012;19:156-160 PMID: 22101905 ↳journal 126 Lussier YA*, Li H. The Rise of Translational Bioinformatics. Genome Biology. 2012, 13:319 ↳journal

Article Rank: #11 of Genome Biology & Rank#37 of any BioMed Journals (9/12/2012; >5300 accesses); 127 Lussier YA*, Li H, M Maienschein-Cline. Conquering computational challenges of omics data and post-

ENCODE paradigms. Genome Biology. 2013, 14:310 ↳journal Article Rank: #4 of Genome Biology & Rank#39 of any BioMed Journals (9/12/2013; >5500 accesses);

128 Lussier YA*, Li H*, Pouladi N, Li Q. Accelerating precision biology and medicine with computational biology and bioinformatics. Genome Biology, 2014, in press.

Invited Conference Papers 129 Lussier YA. "Remote Product Engineer Function in a Product Development Cycle". IBM Canada Administrators

and Engineers Work Term Meeting, Toronto, August 1984. 130 Lussier YA; Rothwell DJ: "Coding panel on SNOMED". Moving Toward International Standards in Primary

Care Informatics: Clinical Vocabulary, American Medical Informatics Association (AMIA) Family Practice / Primary Care Working Group, Intern Med Inform Assoc (IMIA) Working Group V, New Orleans, Nov1-2, 1995.

131 Lussier YA. General Overview of SNOMED and Applications to Primary Care. Moving Toward International Standards in Primary Care Information: Clinical Vocabulary, Conference Summary Report, AMIA Primary Care Working Group, New Orleans, November 1995

Book Chapters 132 Nawar T, Gagne ER, Turcotte R, Lussier YA, Plante GE. Effect of angiotensin converting enzyme inhibition on

thirst and salt-appetite.“ACE Inhibitors”; P D’Orléan-Juste, GE. Plante, ed. Birkhäuser, 2001- 187p. 133 Lussier YA§, Jenders R§, Mendonça EA§: “Clinical Decision Support Systems.” Healthcare Information Systems,

2nd Ed. Best Practices Series, Auerbach, Beaver K ed. Chapter 17, 2003:221-36. [Google Books] 134 Kukafka R, Lussier YA, Cimino JJ. Chapter# 19 “The MI-HEART Project” p.227-238 in "Social Informatics and

Consumer Health: Opportunities and Issues" in Lewis, D., Eysenbach, G., Kukafka, R., Stavri, Z., and Jimison, H. Consumer Health Informatics. Springer-Verlag, New York. 246p. pp.227-238 (2005). [Google Books]

135 Lussier YA*: Chapter 99 on “Ontologies and Natural Language Processing”. Russ Altman, Shankar Subramaniam. Volume 4: Bioinformatics. Encyclopaedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons, (2005 pp. 1-17). ↳hyperlink

136 Lussier YA*, Shortliffe EH: Chapter 22 (Final Chapter): IT-Related Grand Challenges in Medicine and Health”.pp.441-452 HP Lehmann, PA Abbott, NR Roderer, A Rothchild, S Mandell, JA Ferrer, RE Miller, MJ Ball, Editors, “Aspects of the Computer Patient Record”, 2nd Ed. Springer-Verlag, 2006 483p. [GoogleBooks]

137 Lussier YA*, Bodenreider O*. Clinical Ontologies for Discovery Applications. pp.101-119 Chritopher Baker and Kei Cheung, Editors. Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. Springer Verlag 2007, XXII, 450 p. [GoogleBooks] ↳hyperlink

138 Lussier YA*, Crowson M, chapter on “Natural language Processing for Database Systems”, The Encyclopaedia of Database Systems, Springer 2009. Özsu, M. Tamer; Liu, Ling (Eds.) 2009, Approx. 4000 p. ISBN: 978-0-387-49616-0. ↳hyperlink

139 Lussier YA*, Chen J, chapter on “Clinical Ontologies”, The Encyclopaedia of Database Systems, Springer 2009 Özsu, M. Tamer; Liu, Ling (Eds.) 2009, Approx. 4000 p. ISBN: 978-0-387-49616-0. http://www.springerlink.com/content/v903264116q61u81/fulltext.html

140 Mendonça E*, Lussier YA*, chapter "The frontiers of cancer phenomics", book “An 'Omics' perspective of Cancer” , Chapter 11, pp.204-10 Springer, 2010. [GoogleBooks] http://www.springer.com/biomed/book/978-90-481-2674-3

§ These authors have contributed equally to the work.


141 Lussier YA, Li H, chapter on “Hypothesis generation from heterogeneous datasets”, Editor Neil Sarkar, Biomedical Informatics. In press 2013.

Published Refereed Abstracts and Refereed Conference Panels 142 Lussier A; Lebel E; Davis A; Lussier YA: "51Cr Quantitative Evaluation of the GI. Microbleeding with the

Administration of Nabumetone, Aspirin and Placebo". Clinical and Experim Rheumatology, 1987 (5) S-2, p.107. 143 Lussier YA; Plante GE: "Influence de l'alcalose sur la réponse rénale à une surcharge saline". Médecine sciences,

1987(3) 9, Suppl., p.37a. 144 Turcotte R; Lussier YA; Plante GE: "L'appétit pour le sodium". Médecine sciences, 1987(9) 9, Suppl. p.33a. 145 Plante GE; Lussier YA: "Contrôle humoral des volumes de l'organisme". Annual Congress, Société Québécoise

de Néphrologie, Orford, April 29-30, 1988. 146 Lussier YA; Plante GE: "Proximal Reabsorption: A Regulator of Glomerular Filtration Rate". Federation of

American Societies for Experimental Biology (FAZEB), 72nd Annual Meeting, Las Vegas, May 1-5, 1988. 147 Plante GE; Prévost C; Lussier YA; Braquet P; Sirois P: "Hormonal Control of Body Fluid Volumes: Evidence

Supporting the Role of the Atrial Peptide (ANP), Ouabain-like Material (OUAB) and the Platelet Activating Factor (PAF)". 12th Scientific Meeting of the International Society of Hypertension, Tokyo, May 21-28, 1988.

148 Turcotte R; Lussier YA; Plante GE: "L'appétit pour le sodium". Annual Meeting of the Ordre des Chimistes du Québec and the Corporation professionnelle des diététistes du Québec, Montréal, May 26-28, 1988.

149 Lussier YA; Plante GE: "La réabsorption proximale contrôle la filtration glomérulaire". Club de recherches cliniques du Québec, Médecine sciences, no. 4, 1988, p.45a.

150 Lussier YA; Plante GE: "Effets de l'acidose métabolique chronique sur la pression artérielle". Club de recherches cliniques du Québec, Médecine sciences, no. 4, 1988, p.41a.

151 Marineau Y; Lussier YA; Plante GE: "Particularités des effets physiologiques rénaux de l'indapamide". Club de recherches cliniques du Québec, Médecine sciences, no. 4, 1988, p.41a.

152 Marineau Y; Lussier YA; Plante GE: "Effets de l'acidose métabolique sur la production rénale d'eau libre". Club de recherches cliniques du Québec, Médecine sciences, no. 4, 1988, p.41a.

153 Prévost C; Lussier YA; Plante GE: "Réponse rénale et extrarénale à une charge saline isotonique chez le rat". Club de recherches cliniques du Québec, Médecine sciences, no. 4, 1988, p.45a.

154 Plante GE; Prévost C; Lussier YA; Braquet P; Sirois P: "Hormonal Control of Body Fluid Volumes: Evidence Supporting the Use of the Atrial Peptide (ANP), Ouabain-like Material (OUAB) and the Platelet Activating Factor (PAF)". Internat. Soc. Hypertension, Japan, 1988.

155 Lussier YA; Plante GE: "Contrôle tubulaire de la filtration glomérulaire". Annual Congress of the Société Québécoise de Néphrologie, Val-David, April 21-22, 1989.

156 Lussier A; De Médicis R; Lussier YA; Lebel E: "Gastrointestinal Microbleeding Caused by Soluble and Plain Aspirin: Influence of Local and Systemic Factors". 58th Annual Assembly of the Royal College of Physicians and Surgeons of Canada, Clinical and Investigative Medicine, 1989 (12) 4 Supp.B96.

157 Lussier A; De Médicis R; Lussier YA; Lebel E: "Gastrointestinal Microbleeding Caused by Aspirin: Influence of Local and Systemic Factors". XVIIth Internat Congress in Rheumatology (ILAR), Rio de Janeiro, 9/17-23/1989.

158 Lussier A; Lebel E; Gervais P; Lussier YA; De Médicis R: "Gastrointestinal Microbleeding Induced by Flurbiprofen: Effect of Sulcratfate". XVIIth Internat Congress in Rheumat (ILAR), Rio de Janeiro, 9/17-23/1989.

159 Lussier YA; Prévost C; Braquet P; Plante GE: "Progression de l'insuffisance rénale: rôle du facteur d'aggrégation plaquettaire (PAF)". Médecine sciences, Suppl. no 3, 1989, p.47a.

160 Lussier YA*; Desruisseaux B; Bissonnette B; Cadieux P; Dumas G; Lévesque Y; Maksud M; St-Arneault R; Yale PP: "Les Assises Médicales du Dossier-Patient Informatisé". 4ème Journée québécoise de la recherche en médecine familiale, Orford, April 3, 1992.

161 Lussier YA*: "L'amélioration de la rédaction d'observations médicales grâce à un logiciel fonctionnant sur une ardoise électronique". Colloque Parlons Qualité sur l'évaluation de l'exercice professionnel des médecins, Quebec College of Physicians (Collège des Médecins du Québec), Montréal, June 17-19, 1992.

162 Lussier YA*; Desruisseaux B; Dumas G; Bissonnette B; Lévesque Y; Maksud M; Yale PP; St-Arneault R: "L'informatisation du dossier-clinique: une étape vers la description explicite de la syntaxe sémiologique". Médecine sciences 1992 (8) Suppl. no. 2.

163 Yale PP; Lussier YA; St-Arneault R:"Le dossier-clinique informatisé psychiatrique". Scientific Meeting of the Psychiatry Department of the Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, January 29, 1993.


164 Lussier YA*; Desruisseaux B; Dumas G; Bissonnette B; Lévesque Y; Yale PP; St-Arneault R: "Clinical Encounter Filters: A Knowledge-Base Layer Improving the Physician's Data Entry". American Medical Informatics Association (AMIA) 1993 Spring Congress, St-Louis, Missouri, May 9-12, 1993.

165 Smith W; Lussier YA; Fiacco PA; Rusler DC; Naeymi-Rad F: "Panel: Office-Based Computerized Patient Record Vocabulary: Have You Ever Metathesaurus You Didn't Like?" AMIA Spring Symp Proc. 6/9-12/1993.

166 Lussier YA*: "The physician perspective of using a pen-based CPR". The Clinical / Bedside Computing Conference, Toronto, June 28-29, 1993.

167 Lussier YA*: "Description of a Pen-Based Graphical Interface for Physician's Recording Medical Findings". 9th Ann Internat Symp Comput Medical Records, San Antonio, TX 4/21-24/93.

168 Lussier YA*; Côté RA: "L'étude conceptuelle comparée de la nomenclature SNOMED confirme son efficacité à codifier les données médicales". Médecine sciences 1995 (11) no. 2, 1995.

169 Lussier YA*; Côté RA: "Le contenu clinique de SNOMED: l'assise des données médicales électroniques". 7ème Journée québécoise de la recherche en médecine familiale, Montréal, April 24, 1995.

170 Lussier YA*; Côté RA: "A Comprehensive Analysis of SNOMED International Encoding of Symptoms, Signs and the Patient Record Structure". American Med Inform Assoc (AMIA) Spring Congress, Boston , 6/24-28/1995.

171 Lussier YA*; Côté RA: "Harnessing SNOMED: A Relational Database Design for the Computerized Patient Record (CPR)". 19th Ann Symp Comput Appl in Med Care (SCAMC), 1995; IEEE, 1995, p.1019. PMC2579872

172 Moehr JR*; Chute C, Lussier YA, Cimino J, Rossi-Mori A, Kluge E: "Advanced Patient Records and Medical Concepts Representation". Proc 8th World Congress on Medical Inform MEDINFO '95, 12/23-27/1995.

173 Lussier YA*; Côté RA: "SNOMED Encoding of Symptoms, Signs and the Patient Record Structure: The Core of Advanced Medical Records". Proc 8th World Congress on Medical Inform MEDINFO '95, 12/23-27/1995.

174 Moehr J; Lussier YA; Côté RA: "Issues for Classification, Coding in Clinical Documentation in Canada". Canada’s Health Informatics Association COACH Conference 22, Vancouver, April 14-16, 1997.

175 Côté RA*; Lussier YA*; Brochu L: "A Data Structure for Medical Language: the Extended SNOMED Model". Canada’s Health Informatics Association COACH Conference 21 Workshop, Toronto, Ontario, March 30, 1996.

176 Lussier YA*; Rothwell DJ*: "The benefits of a standardized terminology for effective health evaluation". Proc International Health Evaluation Association (IHEA), Victoria, B.C., 10/9-12/1996.

177 Rothwell DJ*; Lussier YA*: "A SNOMED Overview". International Health Evaluation Association (IHEA), Victoria, B.C., October 9-12, 1996.

178 Lussier A; De Médicis R; Lussier YA: "Musculoskeletal System: From the snap diagnosis to the semiologic algorithm". PANLAR Symposium, II ACCA Congress, 11/19-23/1996.

179 Lussier A; De Médicis R; Lussier YA: "Musculoskeletal System: From the snap diagnosis to the semiologic algorithm". VI Meridian Days on Rheumatology, Meridas, Venezuela, Sept 18-20, 1997.

180 Lussier YA*; Côté RA: "Novel Relational Database Design Based on the Systematized Nomenclature of Human and Veterinary Medicine". Canada’s Health Informatics Association COACH Conference 4/14-16/1997.

181 Lussier YA*: “Measuring the Accuracy of a Nomenclature Encoder Supporting Postcoordination” Proc AMIA Annu Symp 1988:1039. PMC2232191

182 Lussier YA§*, Kukafka R§, Cimino JJ: “Overcoming the Barriers of WEB-Based Interventions for Elder Patients: Enabling Strategies for the MI HEART Clinical Trial”. Proc AMIA Annu Symp. 1999:1110. PMC2232633

183 Kukafka R, Lussier YA, Cimino JJ: “Developing and Evaluating Theory-Based Educational Content for WEB Applications”. Proc AMIA Annu Symp. 2000:1056. PMC2243954

184 Chuang J, Kukafka R, Lussier YA, Jenders RA, Cimino JJ: “A Web-Based System For Prediction Of Coronary Heart Disease Risk Using The Framingham Algorithm”. Proc AMIA Annu Symp. 2000:983. PMC2243802

185 Lussier YA*, Wang D, Kukafka R, Cimino JJ: “Improving the Development of Composite Educational Guidelines Using Decomposition of Concept Lattices”. Los Angeles, CA, November 4-8, 2000, AMIA Annu Symp Proc.2000:1073. PMC2243852

186 Lussier YA*, Shagina L, Friedman C: “Automating ICD-9-CM Encoding Using Medical Language Processing: A Feasibility Study”. Los Angeles, CA, Nov. 4-8, AMIA Annu Symp Proc. 2000:1072. PMC2243974

187 Kukafka R, Lussier, YA, Cimino JJ. Evaluating web-based tailored health communications: Illustrations from the MI-HEART project. American Public Health Association Annual Meeting, Atlanta, GA, Oct. 24, 2001.

§ These authors have contributed equally to the work. * Corresponding author


188 Lussier YA*, Kukafka R, Patel VL, Cimino JJ: “Dynamic Cognitive Health History Modeling to Tailor Patient Education: Description of the MI HEART Communications”. MEDINFO 2001.

189 Li J, Lussier YA, Kukafka R, Cimino JJ. Harnessing Web Information Technologies for Secure, Adaptive and Individualized Health Communications. , Proc AMIA Annu Symp 2001:956. PMC2243621

190 Lussier YA*, Kukafka R, Linfane A, Patel VL, Cimino JJ. Lessons Learned in the Early Phase of the MI-HEART Clinical Trial. Proc AMIA Annu Symp 2001:825. PMC2243624

191 Lussier YA*, Kukafka R, Li J, Cimino JJ. MI-HEART: a Comprehensive MgmtSystem to Deliver, Monitor and Measure Efficacy of Individualized Web-based Education. Proc AMIA Annu Symp 2001:1076. PMC2243577

192 Kukafka R, Lussier YA, Patel V, Cimino JJ. The MI-HEART Project: Information Technology (IT) for One-to-One Tailored Patient Communication. AMIA Annu Symp Proc 2001:949. PMC2243592

193 Sarkar IN, Cantor MN, DeSalle R., Lussier YA*. Exploring SNOMED-RT Using Phylogenetic Analysis Tools. AMIA Annu Symp Proc 2002; p.1153. PMC2244147

194 Kukafka R, Lussier YA, Cimino JJ. Evaluating web-based tailored health communications: Illustrations from the MI-HEART project. American Public Health Assoc Ann Meeting, Atlanta, GA, 10/24/2001. Abstract 5069.

195 Choi J, Lussier YA, Mendonça EA. Adapting Current Arden Syntax Knowledge for an Object Oriented Event Monitor. AMIA Annu Symp Proc 2003:914. PMC1479901

196 Tao Y, Mendonca EM, Lussier YA*. A “Systematics” Tool for Medical Terminologies. AMIA Annu Symp Proc 2003;:1028. PMC1480204

197 Kuo T, Mendonca EM, Lussier YA*. Guideline Interaction: a study of interactions among drug-disease contraindication rules. AMIA Annu Symp Proc 2003:901.PMC1480131

198 Lussier YA*, Williams R. Policy Coordination and Automated Communication of Critical Events. 2004 Public Health Information Network, Center for Disease Control. May 24-26, 2004, Atlanta. ↳proceedings

199 Tulipano PK, Tao Y, Zanzanico P, Kolbert K, Lussier YA, Friedman C*.A Molecular Imaging Knowledge Base Using Automated Information Extraction Methods. 3rd Ann Meeting Society for Molecular Imaging, 9/9-12/2004

200 Lussier YA*. Automated Terminological Networks For High Throughput Comparative Biology of Phenotypes. Interface 2004, Computational Biology and Bioinformatics, 36th Symp, Maryland,5/26-29/2004.

Sarkar IN, Cantor MN, Bodenreider O, Lussier YA*. GenesTrace (TM): Biological Knowledge Discovery via Structured Terminology. MEDINFO 2004, p.1842. ↳proceedings

202 Lussier YA*. Overview of Clinical Genomics Technology. SS114 Bringing Context and Consistency to the Genomic Revolution - Creating Visible Man. Ann Meeting of the College of American Pathologist. 9/19-22/2004.

203 Patel C, Lussier YA*. Re-representing Biomedical Ontologies using the Web Ontology Language - A Checklist. Standards and Ontologies for Functional Genomics 2 (SOFG 2). Oct 23, 2004 - Oct 26, 2004,

204 Lussier YA*. Computational Ontologies for High Throughput Visualization and Analyzes of the Phenome. Standards and Ontologies For Functional Genomics 2 (SOFG 2), Oct 23-26, 2004.

205 Lussier YA*. “Impact of Healthcare Practices and Financing on Clinical Informatics Applications and Research: A Proposed Predictive Model”. Internat Colloquium. Reflections and Realities: How Much Impact Has Our Health/Medical Informatics Research Had On Our Health Care Systems? University of Victoria, June 3-4, 2005.

206 Palacios G, Liu Y¥, Hegyi H¥, Jabado O, Renwick N, Briese T*, Lussier YA¥*, Lipkin WI*. Oligonucleotide Microarrays for Virus Detection. Regional Ctrs of Excellence for Biodefense and Emerg Infects Dis Research 2nd Ann Meeting 3/14-15/2005.

207 Büchen-Osmond C, Lussier YA, Lipkin WI. Since 1990: ICTVdB - The Universal Virus Database. Joint Meeting of the 3 Divisions of the InternatUnion of Microbiol Societ, XIIIth Internat Congress Virology. 7/23-28/2005.

208 Lussier YA*, Liu Y, Skolnick J, Gerstein M. Progress of the Biomedical Informatics Core. Annual Meeting of the Northeast Research Center of Excellence in Biodefense and Emerging Infectious Diseases. 2005/9.

209 Tulipano K, Tao Y, Zanzonico P, Kolbert K, Lussier YA, Friedman C. Natural Language Processing in the Molecular Imaging Domain. AMIA Annu Symp Proc 2005;:1143.PMC1560602

210 Lussier YA*, Bodenreider O*, Kashyap V, Patrick TB, Neumann E, Rector A. Panel: Towards a Semantic Web For Life Sciences? AMIA Annu Symp Proc 2005.

211 Borlawsky T, Li J, Jalan S, Stern E, Williams R, Lussier YA*. Partitioning Knowledge Bases between Advanced Notification and Clinical Decision Support Systems. AMIA Annu Symp Proc 2005;:901. PMC1560494

212 Lussier YA*, Li J, Liu Y, Patel C, Hsiao T, Quek HN Computational approaches for genome scale analyses of phenotypes—Bridging the phenotypic gap between clinical repositories and model organism databases. Genome Informatics 2005. p.89. Fri 10/28 - Tue 11/01 2005. Cold Spring Harbor Laboratory.


213 Sam L, Borlawsky T, Rappaport D, Li J, Shagina L, Liu Y, Friedman C, Lussier YA*. Towards a Eukaryotic Phenome: the PhenoGO Database System. Pac Symp Biocomput 2006.

214 Tao Y, Patel C, Friedman C, Lussier YA. Issues in Representing Biological and Clinical Phenotypes Using Formal Models. KR-MED 2006 Proceedings.Vol.222,p.100 ↳proceedings

215 Tao Y, Patel C, Friedman C*, Lussier YA*. OWL-based Interoperation of Clinical and Genetic Phenotypes anchored with the Phenotypes Attribute Ontology of the GO Consortium. “Biomedical Ontology in Action/KR-MED 2006 International Workshop” organized by the National Center for Ontology Research (NCOR), and the American medical Informatics Association (Biomedical Knowledge Working Group –Baltimore Nov 8, 2006.

216 Moreno L, Gomberg-Maitland M, Maitland M, Collins K, Sammani S, Ma SF, Husain AN, Liu Y, Sam L, Lang RM, Ratain MJ, Lussier YA, Garcia JG*.Modulation of Pulmonary Hypertension (PH) by Ser/Thr and Tyr Kinase Inhibitors. International Conference of the American Thoracic Society May 19-24, 2006 San Diego.

217 Tao Y, Li J, Friedman C, Lussier YA*. Predicting New Functions of Human Genes from the Network of Gene Ontology Annotations. Pac Symp Biocomput 2007.

218 Liu Y, Li J, Sam L, Goh CS, Gerstein M*, Lussier YA*. Computational Proteomics: High-throughput Analysis for Systems Biology. Pac Symp Biocomput 2007.

219 Chen J, Lussier YA*. Automated functional classification of Human Disease Genes. Pac Symp Biocomput 2007. 220 Lussier YA*, Friedman C*. BiomedLEE: a natural-language processor for extracting and representing

phenotypes, underlying molecular mechanisms and their relationships. ISMB 2007 (Intelligent Systems for Molecular Biology). http://www.iscb.org/uploaded/css/O02Lussier.pdf

221 Liu Y, Palacios G, Jabado OJ, Hegyi H, Briese T, Lipkin WI*, Lussier YA*. “Cross-Phyla Protein Domain Alignment as a Surrogate for Species-Based Sequence Conservation in Viral Microarray Probe Design”. ISMB 2007 http://www.iscb.org/uploaded/css/I36Lussier.pdf

222 Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA*. An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits'. ISMB 2007 . http://www.iscb.org/uploaded/css/C003Lussier.pdf

223 Liu Y, Li J, Sam L, Lussier YA*. Robust Methods for Accurate Diagnosis Using Highly Multiplexed Microbiological Arrays. ”. ISMB 2007 . http://www.iscb.org/uploaded/css/I20Liu.pdf

224 Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA*. An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Metaphenotypes. 1st Midwest Symposium on Computational Biology and Bioinformatics (MSCBB). http://cbb.northwestern.edu/MSCBB/index.php

225 Chen ES, Lussier YA, Borlawsky TA, Qureshi K, Hripcsak G*. Monitoring the Function and Use of a Clinical Decision Support System. AMIA Annu Symp Proc. 2007 ; :902.

226 Liu Y, Sam L, Lussier YA*. Robust Informatics Methods for Accurate Diagnosis Using Highly Multiplexed Virus Arrays, AMIA Ann Proc. 2007, Oct 11:1039.

227 Sam L, Borlawsky T, Tao Y, Li J, Friedman C, Smith B, Lussier YA. Information-Theoretic Classification of SNOMED Improves the Organization of Context-Sensitive Excerpts from Cochrane Reviews. Proc AMIA Ann 2007:1100. PMC2655812

228 M.L. Maitland, M. Gomberg-Maitland, L. Moreno-Vinasco, L. Sugeng, A.N. Husain, Y. Lussier, S.L. Archer, J.G.N. Garcia, M.J. Ratain. Developing the anti-cancer VEGFR-2/multi-kinase inhibitor sorafenib for treatment of human pulmonary arterial hypertension Keystone Symp Molecular, Cellular, Physiological, and Pathogenic Responses to Hypoxia. January 15 - 20, 2008 • Vancouver.

229 Lang, SN Goonewardena, T Wang, L Moreno-Vinasco, Y Huang, EC Svensson, V Natarajan, P Breysse, A Geyh, JM Samet, YJ Peng, Y Lussier, N Prabakhar and JG Garcia. Particulate Matter Exposure Triggers Ventricular Arrhythmias via Carotid Body/Autonomic Dysfunction in Murine Model of Cardiomyopathy. Central Society for Clinical Research and Midwestern Section American Federation for Medical Research, Ann Meeting, 4/24-25/08, 2008 (Abstract #74). (MWAFMR Centocor Scholar’s Award Winner).

230 NJ Meyer, Y Huang, S Sammani, L Moreno-Vinasco, YA Lussier, AN Husain and JG Garcia,. GADD45A Protects Against Ventilator-Induced Lung Injury. Central Society for Clinical Research and Midwestern Section American Federation for Medical Research, Ann Meeting,4/24-25/08, 2008 (Abstract #82).

231 L Moreno-Vinasco, T Wang, Y Huang, J Linares, G Lang, SN Goonewardena, A Geyh, P Breysse, JM Samet, V Natarajan, Y Lussier and JG Garcia. Murine Pulmonary Responses to Airborne Particulate matter Genomic Analysis and Contribution to Airway Hyperresponsiveness. Central Society for Clinical Research and Midwestern Section American Federation for Medical Research, Ann Meeting,4/24-25/08, 2008 (Abstract #85).

232 RR Reeves, Y Huang, L Moreno-Vinasco, S Sammani, S Hong, S Ma, J Moitra, T Mirzapoiazova, C Evenoski, SQ Ye, YA Lussier and J Garcia. Gene Expression Changes Mediated by Pre-B-Cell Colony Enhancing Factor in


Ventilator-Induced Lung Injury (VILI).Central Society for Clinical Research and Midwestern Section American Federation for Medical Research, Ann Meeting,4/24-25/08, 2008 (Abstract #95).

233 A.A. Desai, L. Moreno-Vinasco, M. Gomberg-Maitland, M. Maitland, P.A. Singleton, S. A.A. Desai, L. Moreno-Vinasco, M. Gomberg-Maitland, M. Maitland, P.A. Singleton, S. Sammani, L. Sam, Y. Liu, A. Husain, R.M. Lang, M.J. Ratain, Y.A. Lussier, J.GN. Garcia. Role of the MAPK Cascade in a Rodent Model of Pulmonary Hypertension. Central Society for Clinical Research and Midwestern Section American Federation for medical Research, Ann Meeting,4/24-25/08, 2008 (Abstract #121).

234 Sammani, L. Sam, Y. Liu, A. Husain, R.M. Lang, M.J. Ratain, Y.A. Lussier, J.GN. Garcia. Role of the MAPK Cascade in a Rodent Model of Pulmonary Hypertension. International Conference of The American Thoracic Society, Toronto May 16-21 2008, #717, p.333 (proceedings).

235 L Moreno-Vinasco, T Wang, Y Huang, J Linares, G Lang, S Goonewardena, A Grabavoy, A Geyh, P Breysse, V Natarajan, J Samet, Y Lussier, JGN Garcia. Murine Pulmonary Responses to Airborne Particulate Matter: Genomic Analysis and Contribution to Airway Hyperresponsiveness. International Conference of The American Thoracic Society, Toronto May 16-21 2008, F109,p.169 (proceedings).

236 S Hong, L Moreno-Vinasco, Y Huang, S Sammani, JW Barnard, J Moitra1, T Mirzapoiazova1, C Evanoski, R Reeves, SQ Ye, YA. Lussier, and JGN Garcia. Essential Role for Pre-B-Cell Colony Enhancing Factor in Ventilator-Induced Mechanical Stress and Acute Inflammatory Lung Injury. Intern Conf of The American Thoracic Society, 2008 F68,p.250 (proceedings).

237 Song, X, Park, S-Y, Zhang, Q, Lussier, YA, Xing,RH, Grassi, MA. Wnt/β-catenin signaling in diabetic retinopathy. American Society for Clinical Investigation (2008).

238 R Reeves, Y Huang, L Moreno-Vinasco, S Sammani, S Hong, J Moitra, T Mirzapoiazova, C Evanoski, SQ Ye, YA Lussier, JGN Garcia. Gene Expression Changes Mediated by Pre-B-Cell Colony Enhancing Factor in Ventilator-Induced Lung Injury (VILI). Intern Conf of The American Thoracic Society,2008 #623, p.A601 (335).

239 G Lang, S Goonewardena, L Moreno-Vinasco, T Wang, E Svensson, P Breysse, Y Peng, Y Huang, A Geyh, V Natarajan, J Samet, Y Lussier, N Prabakhar, JGN Garcia. Particulate Matter Exposure Triggers Ventricular Arrhythmias via Carotid Body/Autonomic Dysfunction in a Murine Model of Cardiomyopathy. Intern Conf of The American Thoracic Society, 2008 Poster #F110, Page 167.

240 N.J. Meyer, M.D., S. Sammani, M.D., L. Moreno-Vinasco, Ph.D., Y.A. Lussier, M.D., Y. Huang, M.D., J.G.N. Garcia, M.D., Chicago, IL Loss of GADD45a Exacerbates Murine Ventilator-Induced Lung Injury (VILI), Intern Conf of The American Thoracic Society,p A601. 622.

241 Lilolios K, Walts A, Li J, Saner D, Solway J, Lussier YA*. Network Modeling grounded on Information Theory Accurately Predicts Future Research Collaborators. 2009 AMIA Summit on Translational Bioinformatics.

242 Mitra S (Mitra, S.)1, Meyer NJ (Meyer, N. J.)1, Huang Y (Huang, Y.)1, Singleton PA (Singleton, P. A.)1, Sammani S (Sammani, S.)1, Moitra J (Moitra, J.)1, Evenosk CL (Evenosk, C. L.)1, Moreno-Vinasco L (Moreno-Vinasco, L.)1, Jacobson JR (Jacobson, J. R.)1, Lussier YA (Lussier, Y. A.)1, Garcia JN (Garcia, J. N.)1. Gadd45a and akt signaling in acute lung injury. J Investigative Medicine 2009(57)3:545

243 Huang Y, Ma SF, Mitra S, Lussier YA, Noth I, Garcia JGN. A Diagnostic Genomic Signature Predicts Progression in Idiopathic Pulmonary Fibrosis. International Conference of The American Thoracic Society, San Diego May 15-20 2009. J Investigative Medicine 2009(57)3:562-563 Astract: 126.

244 Vinasco LM, Lang G, Wang T, Goonewardena S, Huang Y, Svensson E, Natarajan V, Breysse P, Peng Y, Geyh A, Lussier YA, Samet J, Prabakhar N, Garcia JG. Particulate Matter Triggers Ventricular Arrhythmias Via Carotid Body/Autonomic Dysfunction In A Murine Model Of Cardiomyopathy. J Investig Med 2009(57):3,546.

245 Lang G, Wang T, Huang Y, Moreno-Vinasco L, Goonewardena S, Svensson E, Natarajan V, Breysse P, Samet J, Peng YJ, Lussier YA, Prabakhar N, Garcia J. Particulate Matter Triggers Ventricular Arrhythmias And Gene Dysregulation In A Murine Model Of Cardiomyopathy. J Investig Med 2009(57):3,543

246 Mitra S, Meyer NJ, Huang Y, Singleton PA, Sammani S, Moitra J, Evenosk CL, Moreno-Vinasco L, Jacobson JR, Lussier YA, Garcia JN. Gadd45a And Akt Signaling In Acute Lung Injury. J Investig Med 2009(57):3,545

247 Mirzapoiazova T Moitra J, Sammani S, Mambetsariev B, Chiang ET, Evenovski C, Wang T 1, Huang Y, Singleton PA, Watterson M, Moreno-Vinasco L, Lussier YA, Garcia JG. Critical Role For Non-Muscle Mlck In Ventilator-Induced Lung Injury (Vili) . S). J Investig Med 2009(57):3,529-30

248 Lee Y, Lussier YA*, Lee S*. The Correlation of Domain Loss and Nonsense-medicated Decay due to Alternate Splicing. ISMB 2008, Toronto.

249 Ma SF, Huang Y, Mitra S, Lussier YA, Noth I, Garcia JGN. A Diagnostic Genomic Signature Predicts Progression in Idiopathic Pulmonary Fibrosis. Central Society for Clinical Research, Midwestern Section American Federation for Medical Research, 2009, April 23-24, Chicago, Il.


250 X. Song, S.-Y. Park, Q. Zhang, G. Bell, Y.A. Lussier, R.H. Xing, M.A. Grassi, Wnt/β-catenin signaling in diabetic retinopathy. Association for Research in Vision and Ophthalmology 2009.

251 Huang Y, Yang X, Crowson M, Li J, Maitland M*, Lussier YA*. A Pharmacokinomics Study for Prediction of Molecular Mechanisms Underpinning the Side Effect of Kinase Inhibitors. AMIA 2009 Summit Transl Bioinform.

252 Yang X, Xie J, Sun X, Lussier YA*. PGnet: A Novel Method for Predicting Epigenetic Regulatory Networks in Gene Expression Arrays of Acute Lymphoblastic Leukemia. AMIA 2009 Summit Transl Bioinform.

253 Hirshman L, Hunter L, Lussier Y, Wu C. Capturing Knowledge that Spans the translational Gap: What is needed and Why? AMIA 2009 Summit on Translational Bioinformatics.

254 Baker C, Lussier Y, Rost B. Interpretation of Mutations with Semantic Support – A Scientific Session led by the International Society for Computational Biology (ISCB). AMIA 2009 Summit on Translational Bioinformatics.

255 Mann DJ, Oble DA, Lussier Y, Petronic-Rosic V, Shea CR, Duffy KL Clinical decision making based on histopathologic grading and margin status of dysplastic nevi. Am Society of Dermato Pathology 10/2-3/2009.

256 S-B, Sammani S, Moreno-Vinasco L, Barnard JW, Moitra J, Mirzapoiazova T, Evanoski C, Ye SQ, Lussier YA, Garcia JGN*. Recombinant Synergism of Pre-B-cell Colony Enhancing Factor and Ventilator-Induced Mechanical Stress in Acute Murine Inflammatory Lung Injury. American Society of DermPath, 10/1-4/09.

257 Zhang W, GamazonE , R. HuangR ,Duan S, Bleibel W, Welsh M, Lussier YA, Dolan M. MicroRNA Signatures of Cytotoxicity Unveils Molecular Underpinnings of Chemotherapeutic Drug Classes. AMIA 2010 Summit in translational Bioinformatics co-sponsored by ISMB, March 2010, San Francisco; S9,p.16.

258 Chen J, Eulo V, Huang Y, Rehman J, Hariprasad SM, Jager RD, V. Sheth V, Chiranand P, Mojica G, Nicolae DL*, Lussier YA*, Grassi MA*. Study of Genetic Expression in Diabetic Retinopathy Reveals Unique Molecular Fingerprint. Association for Research in Vision and Ophthalmology (ARVO) 2010 meeting.

259 Borlawsky T, Li J, Shagina L, Crowson M, Liu Y, Friedman C, Lussier YA. Evaluation of an Ontology-anchored Natural Language-based Approach for Asserting Multi-scale Biomolecular Networks for Systems Medicine. AMIA 2010 Summit in translational Bioinformatics co-sponsored by ISMB, March 2010, San Francisco

260 Michael A. Grassi, Sudha Ramalingam, Ron Klein, Barbara E.K. Klein, Yves A. Lussier, Nancy J. Cox, Dan L. Nicolae. Genome-wide Association Studies for Predisposition to Severe Diabetic Retinopathy Reveal Novel Susceptibility Loci. Association for Research in Vision and Ophthalmology (ARVO) 2010 meeting.

261 Ma SF, Huang Y, Wade SM, Lussier YA, Ammosova T, Machado RF, Gordeuk VR, Garcia JGN. Multivariate genomic analyses predict the presence of pulmonary hypertension in Chuvash with polycythemia. International Conference of the American Thoracic Society, May 14-19 New Orleans 2010.

262 Zhang W, Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, Dolan ME. An integrative approach to predicting human microRNA targets. Amercian Society for Human Genetics, Nov 2010, Washington DC.

263 Yang X, Lee Y, Lussier YA*. Common MicroRNA-mRNA Regulatory Biomodules Predicted in Human Epithelial Cancers. 2010 AMIA Summit on Translational Bioinformatics, p.75.

264 Yang X, Lussier YA*. Common MicroRNA-mRNA Regulatory Biomodules Predicted in Human Epithelial Cancers. AMIA 2010 Summit in Transl Bioinform. March 2010, San Francisco; Track 1, p.26. ↳hyperlink

265 Chen J, Lussier YA*. Mechanism-anchored Prognosis Meta-Signature of Breast Cancer unveiled by Protein Interaction Networks. AMIA 2010 Summit in Transl Bioinform, March 2010, San Francisco; S14, p.18. ↳hyperlink

266 Lee L, Yang X, Huang Y, Fan H, Zhang Q, Wu Y, Li J, Hasina R, Lingen M, Gerstein M, Weichselbaum R, Xing HR, Lussier YA*. Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis. AMIA 2010 Summit in Transl Bioinform 2010, San Francisco; S12,p.17. ↳hyperlink

267 Lee Y, Yang X, Huang Y, Fan F, Zhang Q, Wu Y, Li L, Hasina R, Cheng C, Lingen M, Gerstein M, Weichselbaum R, Xing H, Lussier YA*. Computational Phenomics and Thorough Biological Characterization Uncovers a Tumor Suppressor microRNA and its Regulatory Network. AMIA 2010 Summit in translational Bioinformatics co-sponsored by ISMB, 2010:S16,p.19. http://summit2010.amia.org/files/symposium2008/AMIA_TBI_On-Site_Program.pdf

268 Yang X§, Lee Y§, Huang Y, Chen J, Xing HR* , Lussier YA*. Stromal Microenvironment Processes Unveiled by Biological Component Analysis of Gene Expression in Xenograft Tumor Models. Proceedings of the 2010 AMIA Summit on Translational Bioinformatics, pp. 42. http://summit2010.amia.org/files/symposium2008/AMIA_TBI_On-Site_Program.pdf

269 Lussier YA*, “Hypothesis-Driven Translational Bioinformatics and Targeted Therapy of Head and Neck Cancers”. Translational Bioinformatics for Personalizing Healthcare. Asia Pacific Bioinformatics Conference (APBC), Translational Bioinformatics for Personalizing Healthcare, 1/13/ 2011, Incheon, Korea

270 Reveals Essential Pathways in Disease Recurrence. GU ASCO. 2011 Genitourinary Cancers Symposium, American Society of Clinical Oncology, Feb. 17-19, 2011; Orlando, Florida, USA

271 Chen J, Stadler W, Lussier YA*. Protein-Network Modeling of Prostate Cancer Gene Signatures. 2011 AMIA Summit on Translational Bioinformatics (TBI), San Francisco, March 7-9, 2011.


272 Yang X, Li J, Lee Y, Lussier YA*.,GO-Module: functional synthesis and improved interpretation of biologically or clinically prioritized Gene Ontology terms. 2011 AMIA Summit on Translational Bioinformatics(TBI), San Francisco, March 7-9, 2011.

273 Yang X*, Li J*, Lee Y, Lussier YA*. Novel Genome-wide Array for Conducting Species-Specific Expression of Human Cancer Cell and Mouse Stroma in Xenograft models. 2011 AMIA Summit on Translational Bioinformatics (TBI), San Francisco, March 7-9, 2011.

274 Burton M, Saner D, Yang X, Li H, Solway J, Lussier YA. The dynamic edges of the evolving social network: new collaborations predicted with Information Theory. 2011 AMIA Summit on Clinical Research Informatics (CRI), San Francisco, March 9-11, 2011.

275 Li H, Lussier YA. 2011 AMIA Summit on Clinical Research Informatics (CRI), 3/9-11/2011. 276 Ma SF, Huang Y, Lussier YA, Noth I, Grigoryev DN, Solovyeva M, Hassoun PM, Ammosova T, Desai AA,

Machado RF, Gordeuk VR Garcia JGN. Gene Expression Profiling In Peripheral Blood Mononuclear Cells Correlates With Chuvash Polycythemia Progression To Pulmonary Hypertension. Amer Thoracic Soc 2011.

277 Wang XK, Regan KE, Lee Y, Li J, Lussier YA. Functional concordance of unique event polymorphisms between Mendelian and complex inheritance for predicting personal genome mutations. Personal Genomes Sept 30-Oct 2, 2011. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

278 Peter J. Embi, Yves Lussier, Umberto Tachinardi, MD, The Chief Research Information Officer (CRIO): Early experiences with a new leadership role for academic health centers. AMIA CRI Summit 2012.

279 Complex-disease networks of trait-associated single-nucleotide polymorphisms unveiled by information theory. ISMB 2012, Long Beach, July 15-17th.

280 ISMB workshop Computational Drug Repositioning and Systems Pharmacology. "Rescuing targeted compounds with combination therapy and protein interactions models". Sunday 15 July 2:30-4:25. ISMB 2012, Long Beach, July 15-17th.

281 Regan K, Yang X, Li H, Li J, Huang Y, Lussier YA. Expression-anchored Gene Ontology Signature Predicts Clinical Outcome in Lung Adenocarcinoma Patients. American Medical Association RFS/MSS/IMG Medical Student Section (MSS), in coordination with the Resident and Fellow Section (RFS) and effective 2012 for International Medical Graduates Section (IMGS), ECFMG-certified members (awaiting residency). ★ Best poster award (among 400) ↳hyperlink

282 Peter J. Embi, Umberto Tachinardi, Yves Lussier, Justin Starren, Jonathan Silverstein, "Integrating Governance of Research Informatics and Healthcare IT Across an Enterprise: Experiences from the Trenches”. AMIA Summits Transl Sci Proc. 2013; 2013: 60–62. PMCID: PMC3845750

283 Li H, Lee Y, Li J, Chen JL, Rebman E, Lussier YA. Complex Disease Networks of Trait-Associated SNPs Unveiled by Information Theory. 2011 AMIA Annu Symp Proc • accepted as outstanding and recommended for JAMIA publication.

284 Wang K, Regan K, Li J, Lee Y, Lussier YA*. Mechanism Concordance and Network Models of Mendelian and Complex Inheritance Predict Uncharacterized Trait-Associated Unique Event Polymorphisms. Translational Bioinformatics Conference 2011. Seoul, Korea. • recommended for JAMIA publication.

285 Lee Y, Chen J, Hsu A, Yang X, Li J, Parinandi G, Lussier YA*. Curation-Free Biomodules Mechanisms in Prostate Cancer Predict Recurrent Disease. Translational Bioinformatics Conference 2012. Jeju, Korea. • recommended for BMC Genomic Medicine publication.

286 Lee Y, Li H, Li J, Rebman E, Regan KE, Gamazon ER, Chen JL, Yang X, Cox NJ, Lussier YA. Network Models of GWAS Uncover the Topological Centrality of Protein Interactions in Complex Disease Traits . Translational Bioinformatics Conference 2012. Jeju, Korea. ★ Best Paper Award ↳hyperlink • recommended for J Am Medic Inform Assoc publication.

287 BD Eugenio, C Lugaresi, GM Keenan, YA Lussier, J Li, M Burton, C Friedman, AD Boyd, “HospSum: Integrating physician discharge notes with coded nursing care data to generate patient-centric summaries” Proc AMIA Annu Symp, Washington DC, November 16-20th, 2013 (in press).

288 TY Seiwert, D Atkins, F Worden, JL Wade, BG Sleckman, K Price, T Fitch, K Curtis, J Zavala, T Karrison, Y Lussier, W Stadler, E Vokes, EEW Cohen. A randomized Phase II study of temsirolimus +/- cetuximab in patients with cetuximab-resistant recurrent/metastatic head and neck cancer. ESCO 2013

289 BD Eugenio, C Lugaresi, G M Keenan, YA. Lussier, J Li, M Burton, C Friedman, A D. Boyd, “HospSum: Integrating physician discharge notes with coded nursing care data to generate patient-centric summaries”


American Medical Informatics Association AMIA 2013 Annual Symposium, Washington DC, , 2013. 290 JS Zaman, LWilliams, SR Chae, H Nam, J Li, Y Lussier, Rachel Caskey, MD, MAPP2 and AD Boyd. The

Transition To ICD-10-CM, Challenges For Pediatric Practice. American Academy of Pediatrics National Conference. Orlando, 2013.

291 YA Lussier, AD Boyd. Mitigating Tools for ICD-10-CM Transition Through Convolution and Entanglement. HIMSS conference. Orlando Feb 23-7, 2014.

292 Gardeux V, Achour I, Maienschein-Cline M, Parinandi G, Pesce L, Li J, Li H, Foster I, Garcia JGN, YA. Lussier*. “N-of-1-pathways” unveils personal deregulated mechanisms from a single pair of RNA-seq samples: towards precision medicine. Translational Bioinformatics Conference 2013. Seoul Oct. ★ Best Paper Award ↳hyperlink • recommended for J Am Medic Inform Assoc publication.

293 Gardeux V, Arslan AD, Achour I, Ho TT, Beck WT*, Lussier YA*. “Concordance of deregulated mechanisms unveiled by N-of-1-pathways in underpowered experiments: PTBP1 knockdown case study”. Translational Bioinformatics Conference 2013. Seoul Oct.

294 Yang X, Huang Y, Lee Y, Gardeux V, Achour I, Regan K, Rebman E, Li H, Lussier YA*. In Silico Cancer Cell versus Stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment. Translational Bioinformatics Conference 2013. Seoul Oct. ↳supplements

295 WT Beck, X He, AD Arslan, T-T Ho, V Gardeux, I Achour, K Terai, Y Lussier, A Dudek. Splicing factors as novel therapeutic targets in ovarian and breast cancer. Delhi.

296 Apoorva Chawla, Douglas Adkins, Francis P. Worden, Krishna A. Rao, H. Shawn Hu, Katharine Andress Rowe Price, Jose D Zavala, Theodore Karrison, Walter Michael Stadler, Victoria Meucci Villaflor, Yves A. Lussier, Everett E. Vokes, Ezra E.W. Cohen, Tanguy Y. Seiwert; The University of Chicago Medicine and Biological Sciences, Chicago, IL; Washington University School of Medicine in St. Louis, St. Louis, MO; University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; Southern Illinois University School of Medicine, Springfield, IL; St. John's Mercy Medical Center, St. Louis, MO; Mayo Clinic, Rochester, MN; University of Illinois Hospital and Health Sciences System, Chicago, IL; University of California, San Diego, San Diego, CA Effect of the addition of temsirolimus to cetuximab in cetuximab-resistant head and neck cancers: Results of the randomized PII MAESTRO study. Background: Patients with cetuximab resistant HNC have a median PFS of only 1.8 months (deSouza 2012). Preclinical/computational modelling suggests synergy between mTOR and EGFR, and potential to overcome resistance and aberrations in the PI3K-MTOR pathway occur in ≥30% of HNC. A previous trial of erlotinib+everolimus was terminated early due to toxicity (Bauman 2013). Methods: Eligibility was PS≤1, metastatic HNC with documented progression on cetuximab. Pts were randomized to temsirolimus (T) 25 mg +/-cetuximab (C) 400/250 mg/m2 weekly. Primary endpoint was PFS with a target of 80 pts to detect a 2 months increase. 2nd endpoints were RR, OS, toxicity. Results: 80 pts (40 TC, 40 T) started treatment via the Univ. of Chicago, and Mayo Phase II CTEP networks. Median age was 63 yrs; 69M, 11F. Median PFS was 89 days (TC) vs 93.5 days (T), NS. Median overall survival was 205/181 days, NS. Treatment was tolerable with fatigue, skin and hematologic toxicities being common. Hyperglycemia was seen in 17/80 patients (11 TC, 6 T). Grade 3-4 toxicities included metabolic abnormalities (17/40 TC, 10/40 T), hematologic toxicity (7/40 TC, 13/40 T), infection (4/40 TC, 3/40 T), and pulmonary toxicity (2/40 TC, 2/40 T). 5 responses (1 CR, 4 PR) were observed in the TC arm (RR 12.5%) (TC) vs 1 PR (2.5%) on T arm (one-sided P=0.1). Of note, all TC responders had disease control from prior C treatment (response/prolonged SD) with subsequent acquired resistance. In responders the mean interval between C failure and start of trial treatment was 3.4 months (1.1 – 6.5). In TC responders, median duration of response was 7.2 months (5.1 – 15.3). Interestingly, TC responses were maintained for up to 15 months exceeding prior benefit from C in several pts. TC responders had a median PFS of 231 days. The sole T alone response was short (89 days). Conclusions: T+C is safe and tolerable. The addition of T to C appears to overcome acquired C resistance in 12.5% of pts despite an overall negative trial. Responses are durable and clinically meaningful in this otherwise poor prognosis population. Single agent T is ineffective. Prior benefit from cetuximab is a candidate predictive biomarker for benefit from TC. Clinical trial information: NCI 8692. J Clin Oncol 32:5s, 2014 (suppl; abstr 6089)

297 TUTTLE M, LUSSIER YA. What's In A Name: Precision Medicine and a New Nosology . In 2012 the National Research Council published a white paper[1] on the need for a new taxonomy of disease, noting the failure of our current disease names to address the needs of precision medicine, based on a deeper understanding of nosology and the requirements of personalized medicine. The panel will discuss the implications of this call in several ways. Dr. Lussier will discuss promising translational bioinformatics innovations in precision therapeutics. Dr. Bernstam will discuss the importance of finding actionable abnormalities in the genome of the tumors she treats with precision. Dr. Nelson will discuss how this new knowledge can be incorporated into the Bloisian model of disease descriptions[2] as well as how the “classical” patient findings can be used to further develop these descriptions. Mr. Tuttle will discuss the growing experience with supervised


and unsupervised machine learning as a tool of discovery, and the application of this paradigm to nosology. AMIA FALL SYMPPOSIUM

Invited Scientific and Grand Round Lectureships -See page 5 for Conference Keynotes and Commencement lectureships

-Peer Reviewed Highlight Papers 298 Highlights of 2007 (ISMB). An integrative genomic approach to uncover molecular mechanisms of prokaryotic

traits. (213 submissions, 10% acceptation rate). 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB). ↳hyperlink

299 AMIA STB Late Breaking News 2010- Computational Phenomics and Thorough Biological Characterization Uncovers a Tumor Suppressor microRNA and its Regulatory Network. AMIA 2010 Summit on Translational Bioinformatics, San Francisco, March 2010.

300 Highlights of 2011 (ISMB). Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis. (10% acceptation rate). 19th Ann Internat Conf on Intellig Syst Mol Biol. ↳hyperlink

301 AMIA STB Late Breaking News 2011- " Therapy Targeted at Unique Personal Disease Polymorphism Using Mechanistic Concordance between Mendelian and Complex Inheritance Anchored on Protein Domain Interactions". AMIA 2011 Summit on Translational Bioinformatics, San Francisco, March 2011.

302 ISMB Late Breaking News 2012. Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer 20th Ann Internat Conf on Intelligent Systems for Mol Biol, Long Beach 7/15/12.

-Invited Conference Speaker 303 "Combination therapy for rescuing targeted Erlotinib therapy in oral cancers: from in silico models to clinical

trial". 4th meeting on Drug Repositioning, March 14, 2012 in Philadelphia. 304 “The Emergence of Genomic Pathways and Interaction Network Tests in Personal Therapy”. Individualizing

Medicine Conference 2012. Theme 2. Individualizing Clinical Care. 10/1-3/12, Mayo Civic Ctr, ↳hyperlink 305 PERSONALOME: identifying clinically actionable 'Omics. 10/10/13 Realizing the Potential of Precision

Medicine. Opening Keynote. New York

- Guest Speaker at International Institutions 306 International Guest Speaker. First Technical Theme-Biomedical Informatics, Agency for Science, Technology

and Research (A*Star),Singapore, Feb 10 2003. 307 3rd International Symposium of the National Institute of Informatics of Japan, “e-Biology Initiative: Towards

New Frontiers of Biology”, Computational approaches to high throughput analyses of non-molecular phenotypes, Tokyo, 3/10/2005. ↳hyperlink

308 Genome Quebec - “Bridging the Phenotype Gap: Ontology-Anchored Computational Methods for Biomedicine”. Knowledge-Based Bioinformatics Workshop Hosted by the Genome Québec funded project: Ontologies, the semantic web and intelligent systems for genomics. September 21st - 23rd 2005; Montréal, Québec, Canada.

309 DAGSTUHL Seminar Speaker 07132–“Ontology Interoperability: All you need is statistics” / ‘Toward Interoperability of Biomedical Ontologies’, 27.03.2007-30.03.2007. ↳hyperlink

310 Key State Laboratory of Bioelectronics. Computing with ontologies in the practice of medicine and in disease gene discovery , (Chien-Shiung Wu Laboratory), Southeast University, Nanjing, 8/20/08

311 University of Science and Technology of China, Hefei. Computing with ontologies in Systems Biology and in disease gene discovery. School of Life Sciences, China (http://www.ustc.edu.cn/en/), 8/24/08.

312 Ewha Womens University, Hypothesis-Driven Translational Bioinformatics and microRNA-204 regulatory network in Head and Neck Cancers”. Seoul, 1/11/2011,

313 KAIST- Korea Advanced Inst of Science & Technol, 1/14/2011, “Hypothesis-Driven Translational Bioinformatics and Regulatory Networks of Head and Neck Cancers”, Daedeok Science Town, Daejeon, South Korea.

314 Ajou University College of Medicine, Hypothesis-Driven Translational Bioinformatics & High Throughput Phenomics, Suwon, South Korea, 1/14/11.

315 2011 AAPS Annual meeting and Exposition (Am. Assoc. of Pharmaceutical Scientists). Kinase Inhibitor Toxicities Imputer from Kinome and Clinical Trial Data. Session Title: Ascpt/aaps Joint Symposium: Systems


Pharmacology for the Assessment and Prediction of Adverse Drug Effects (#199). Washington Convention Center DC. Oct 26th 2011.

- Scientific Grand Rounds and Seminar Speaker in Universities and Nonprofit Organizations 316 American College of Pathology “Meet the Early Adopters: Lessons Learned and Benefits Gained”. - SNOMED

Users’ Group Conference, Los Angeles, CA, Nov. 3, 2000. 317 Columbia Seminar Speaker. Decision Making at the Moments of Individual and Collective Survival Crisis.

University Seminar on Computers, Man and Society, Columbia University, March 2 2001. 318 NIH/NCI Center for Bioinformatics Seminar, Ontologies and Terminologies in Biomedical Research. Desiderata

for Original and Classical Data Sharing and Reuse. Washington. 3/31/03. 319 Univ of Buffalo Ctr of Excellence in Bioinform “Phenotypic Networks and the Art of Bioinformatics”. 5/6/2004. 320 Jackson Lab Mouse Genome Informatics, “Biomedical Informatics Tools for Curators”, 6/29/2004, Bar Harbor. 321 Rockefeller Seminar Speaker. Seminars in Clinical Research series at The Rockefeller, University. Computational

Methods for Systems Biology and Medicine: Approaches to high throughput analyses of phenotypes”, 3/30/2005. 322 Harvard Seminar Speaker. Computational approaches for high throughput analyses of phenotypes: bridging the

gap between clinical medicine and genome biology, Computational Biology Group at the Bauer Center for Genomics Research, Harvard University, 6/20/ 2005.

323 The University of Texas Health Science Center at Houston “Hypothesis-Driven Computational Methods for Molecular Medicine and Systems Biology: Genome Scale Integrative Analyses of Phenotypes”. School of Health Information Science in, 6/8/2005.

324 Northwestern University Medical School, Center for Genetic Medicine and Dept. of Cell and Molecular Biology “Computational approaches for genome scale analyses of phenotypes: bridging the phenotypic gap between clinical repositories and model organism databases”, 6/13/2005.

325 University of Chicago Dept. of Pathology “Computational approaches for genome scale analyses of phenotypes: improving the understanding of biological systems and the diagnosis of diseases”, 6/12/2005.

326 Vanderbilt University Dept of Biomedical Informatics, “Systems Biology approaches to the Metagenomic Analysis of Phenotypes”. 8/11/2005.

327 University of Southern California Computational Biology Seminar, Division of Molecular and Computational Biology, Dept. Computational Biology & Bioinformatics, “Phenomic Data and its Valuation Chain”1/18/2007

328 Interface 2007,” Ontology Similarity Networks and Database Interoperability” , 6/23/2006, Philadelphia. 329 AACR Cancer Health Disparity Meeting 2007, “Computational Systems Biology approaches to Elucidating

Functional Mechanisms Underpinning Molecular Profiles of Cancers’ (invited abstracts), 11/ 27/2007, Atlanta. 330 ISMB C-SHALS, Conf on Semantics in Healthcare and Life Sciences of the Internatl Society for Comput Biol.

“Clinical Monitoring: Ontology-Anchored, NLP-Enabled, User-Directed Pharmacovigilence”. 3/5-7/2008. 331 Grand Rounds of the Ctr for Comput Biol & Bioinform of Indiana University School of Medicine, “Networks,

Protein Interactions and Diseases”. 4/14/2008. 332 City of Hope Cancer Center. “Systems Biology of microRNAs in Cancer: A case study of Biomolecular

Networks and Functional Modules” 6/2008. 333 University of Michigan Health Informatics Grand Rounds. "A report of hypothesis-driven translational

bioinformatics: conceived in silico, corroborated in vitro/in vivo, and awaiting confirmation in an approved Phase II Clinical Trial". 10/14/2009.

334 Northwestern Univ Genome Ctr "Steering translation of hypothesis-driven bioinformatics: conceived in silico, corroborated in vitro/in vivo, and awaiting confirmation in an approved Phase II Clinical Trial". 10/29/2009.

335 Arizona State University Dept. of Biomedical Informatics "A tale of hypothesis-driven translational bioinformatics: from computational models to clinical trial". 12/17/2009.

336 Washington University School of Medicine, Division of Statistical Genomics, Genetic Seminar Series, Modeling Systems Biology of Complex Traits in the post-GWAS era. 11/19/2009.

337 Medical College of Milwaukee, Hypothesis-driven translational bioinformatics acceleration pipeline in silico, in vitro, in vivo, and in clinical trial". 11/3/2009.

338 Dartmouth College and Dartmouth-Hitchcock Norris Cotton Cancer Center. “Beyond Synergies, Hypothesis-Driven Translational Informatics as a Catalyst in Targeted Therapy Development” Nov 30th 2010.

339 University of Vermont Grand Rounds of Informatics, “Hypothesis-driven translational bioinformatics: from in silico models to clinical trials with transit in vitro and in vivo” 12/7/2010.


340 Marshfield Clinic Genetics Seminar, “Network modeling of therapeutic resistance initiates Phase II trial in oral cancer". 4/6/2011.

341 University of Illinois in Chicago School of Medicine Center for Evidence-based Practice in the Underserved and the Reducing Health Disparities Through Informatics (RHeaDI). “Network models of therapeutic resistance and personal genomics in clinical practice” 4/14/2011.

342 Biomedical Informatics program of University of Wisconsin-Milwaukee and Medical College of Wisconsin, “Network models of therapeutic resistance translated in vitro, in vivo and in clinical trials” 5/2011.

343 Guest-Speaker FDA - Center for Drug Evaluation and Research (CDER)- Committee for Advanced Scientific Education (CASE) Seminar. DC 10/12/2011.

344 Grand Rounds of The Dept. of Biomedical Informatics, Ohio State Medical Center, Dec. 2011. “Network Models of Mesophenotypes for Personal Genomics and Targeted Therapies” .

345 ASCPT-AAPS Symposium at the 2011 Annual Meeting of the American Association of Pharmaceutical Scientists. Session: Systems Pharmacology for the Assessment and Prediction of Adverse Drug Effects. “Kinase inhibitor toxicities imputed from kinome and clinical trial data” Washington DC 10/26/2011

346 Yang X, Regan K, Huang Y, Zhang Q, Li J, Seiwert TY, Cohen EEW, Xing HR, Lussier YA. Single sample expression-anchored mechanisms predict survival in head and neck cancer. University of Illinois Cancer Research Forum Mar 6, 2012. University of Illinois at Chicago, Chicago, IL.

347 Grand Rounds of The Dept. of Biomedical Informatics, Cancer Cell Biology seminar, West Virginia University Health Science Center and Randolph Cancer Center, April 25th 2012 “Functional Phenotypes and Network Models in Personal Genomics and Targeted Therapies.

- Seminar Speaker at For Profit Corporations 348 IBM Watson Research Laboratory Computational Biology Seminar "Knowledge Technologies for Clinical and

Post-Genomics IT Interoperability". Yorktown, NY, 6/19/2002. 349 First Genetic Trust, Database Schema for Clinical Genomics. Sept. 2003, New Jersey. 350 IBM Watson Laboratories, “Phenomic Program” . Hawthorne. 11/3/2004. 351 IBM Watson Research Center, “Research Technical Discussions on Ontologies in Biomedicine”, Industry

Solution Laboratory, Hawthorne, NY, 7/8/2005. 352 Philips Research “Decision Making & Individual. Healthcare: Managing Inform R&D to achieve ROI”, 10/8/08 353 IPSEN Pharmaceutical June 2014. Title: Clinically actionable “Omics”: the personalome for Precision

Therapy. Abstract: Translating biomolecular modules to clinical practice remains challenging, espescially when their constituent molecular organization is discovered from analysis and integration of genomic, transcriptomic and proteomic assays. This presentation describes how stratification of patients can be derived from computational “omics” studies with case reports of biologically validated tumor genes and a clinical trial of a repositioned therapy. Further, I will demonstrate new approaches to interpret an individual human transcriptome (mRNA), beyond classical genomic (DNA) level analyses. “ontology transforms,” which we define as the often-overlooked model transformations that can be performed over ontology-encoded datasets. The implication of moving to personal prediction integrating the dynamics of the genome (mRNA) with its blueprint (DNA) are numerous: from peripheral blood “omics provocation” essays to predicting individual response to therapy. I will present a cost-effective method of toxicity prediction, a case report of NIH-funded clinical trial confirming bioinformatically-predicted drug repositioning & drug rescue. I will point out the pre-requisite computational foundation for faster and more accurate systems pharmacology: BIG DATA MGMT (information & knowledge storage, integration & reuse).

354 Chongqing University. The practice of personalized medicine: from electronic medical records to clinical genomics and precision therapy. Translating biomolecular modules to clinical practice remains challenging, especially when their constituent molecular organization is discovered from analysis and integration of genomic, transcriptomic and proteomic assays. This presentation describes how stratification care of patients can be improved through the use of electronic medical records coded in rational clinical data representation (ontologies). I will also address how the sciences of computation and genomics can further individualize therapy with a case report of biologically validated tumor genes and a clinical trial of a repositioned therapy. I will demonstrate new approaches to interpret an individual human transcriptome (mRNA), beyond classical genomic (DNA) level analyses. “Ontology transforms,” which we define as the often-overlooked model transformations that can be performed over ontology-encoded datasets. The implication of moving to personal prediction integrating the dynamics of the genome (mRNA) with its blueprint (DNA) are numerous: from peripheral blood


“omics provocation” essays to predicting individual response to therapy. I will point out the pre-requisite computational foundation for faster and more accurate systems pharmacology.

355 Key National Laboratory of Bioinformatics, Shanghai. Precision medicine: translating genomics to clinical applications using networks and ontologies. Translating biomolecular modules to clinical practice remains challenging, especially when their constituent molecular organization is discovered from analysis and integration of genomic, transcriptomic and proteomic assays. This presentation describes how the sciences of computation and genomics can further individualize therapy with a case report of biologically validated tumor genes and a clinical trial of a repositioned therapy. I will demonstrate new approaches to interpret an individual human transcriptome (mRNA), beyond classical genomic (DNA) level analyses. For example, network modeling identified synergy between mTOR and EGFR, with potential to overcome resistance and aberrations in the PI3K-MTOR pathway that occur in ≥30% of head adenocarcinomas (subsequent NIH-funded clinical trial). “Ontology transforms,” which we define as the often-overlooked model transformations that can be performed over ontology-encoded datasets. The implication of moving to personal prediction integrating the dynamics of the genome (mRNA) with its blueprint (DNA) are numerous: from peripheral blood “omics provocation” essays to predicting individual response to therapy.

- Clinical Grand Rounds and Invited Clinical Lectures 356 One-Day Postgraduate Course on Computers in Medicine from the Royal College of Physicians and Surgeons of

Canada, Halifax, Sept. 26, 1996. Internet workshops, "Computer basics for beginners". 357 “Introduction à l’Internet pour la médecine interne et spécialisée”. Seminar, Department of Medicine, Faculté de

Médecine, Université Laval, Quebec City, PQ, February, 1997. 358 "Introduction à l'Internet pour le médecin omnipraticien". Medical Education, Fédération des Médecins

Omnipracticiens du Québec, Sherbrooke, May 1, 1997. 359 "Introduction to the Internet and Related Software: Medical Terminologies : from ICD to SNOMED and its Use

in Computerized-Patient Records for Research and Office Use". Postgraduate course on Computers in Medicine from the Royal College of Physicians and Surgeons of Canada, Vancouver, Sept. 25, 1997.

360 “Methods and preliminary results of the MI-HEART Clinical Trial.” Grand Rounds, St. Vincent's Hospital, Bridgeport, CT, Nov. 27, 2001.

361 School of Medicine, Univ of Sherbrooke. “Architecture génomique et applications cliniques de la thérapie de precision”.

Intramural Lectures -Annual Consortium & Seminar Speaker

362 Univ of Sherbrooke Seminars, "La SNOMED: l'assise de la recherche médicale informatisée". 6/5/95. 363 Université Laval Seminar, Department of Medicine, Faculté de Médecine, “Introduction à l’Internet pour la

médecine interne et spécialisée”., Quebec City, PQ, February, 1997. 364 Medical Education, Fédération des Médecins Omnipracticiens du Québec, Introduction à l'Internet pour le

médecin omnipraticien. Sherbrooke, May 1, 1997. 365 Toyota Technological Institute at Chicago "Collecting and Integrating Phenotypic Information from Multiple

Databases for Correlation with Genomic Databases” 4/10/2006. 366 Computation Institute, Univ.of Chicago. “Systems Properties in a Comprehensive Genomic Networks”. 8/2006. 367 Annual Computation Institute Fellows meeting “Emerging Systems Properties in High Throughput Phenomic

Studies”, Mathematics for Syst Biol Seminar Series: Emergence in Complex Systems Univ of Chicago, 2/21/2007. 368 Annual meeting of the National Research Center for Multiscale Analyses of Genomic and Cellular Networks

(MAGNET) Predictions of Phenotypic Biomodules in Protein Interaction Networks, Wavehill, NY, 4/6/2007. 369 University of Chicago Gastro Enterology Research Conference “Computational Systems Biology approaches to

Elucidating Functional and Molecular Mechanisms of Diseases”, 12/6/2007. 370 University of Chicago CTSA Biological Translational Research Workshops Presentation. Protein Interaction and

Diseases, a year’s review. 3/31/2008.


371 Annual meeting of the National Research Center for Multiscale Analyses of Genomic and Cellular Networks (MAGNET), A tale of hypothesis-driven translational bioinformatics: conceived in silico, confirmed in vitro, established in vivo and awaiting FDA approval for Phase II Clinical Trial. New York, NY, 3/13/2009.

372 Informatics Colloquium of the Dept. of Health Informatics, University of Illinois at Chicago, Feb 28th 2012 “Genome-wide Network Models as Underpinning Mechanisms of Personal Therapeutics”

373 UIC Bioengineering Seminar, University of Illinois at Chicago, March 9 2012 “Genome-wide Network Models for Elucidating Mechanisms of Disease and Therapy”

374 “Network modeling for drug rescue and gene function discovery: from in silico studies to clinical trials”. Center for Pharmaceutical Biotechnology Seminar Series, University of Illinois at Chicago, Jan 24th 2013.

375 “Intergenic DNA’s role in complex disease unveiled by supercomputer-obligated analyses of BIG data”. Computation Institute of the University of Chicago and Argonne Lab. 2013.

376 “The Emergence of Genomic Pathways and Interaction Network-Based Decisions in Personal Therapy”. Institute for Pulmonary Respiratory Medicine Seminar Series, University of Illinois at Chicago, Feb 16th 2013.

377 “Personalome: clinically actionable 'Omics ”, Lung Cancer Seminars, University of Illinois at Chicago, Sept 27th 2013.

378 Clinically actionable “ Omics”: the Personalome for Integrative Medicine. Telemedicine U of Arizona Cancer Center. Translating genomic and molecular bioinformatics discoveries into clinical practice remains challenging. This presentation describes “ontology transforms,” which we define as the often-overlooked model transformations that can be performed over ontology-encoded datasets. We will then show ontology-transforms in action with several scientific examples. For example, we hypothesized a network-based mechanism of resistance of head and neck cancers. We identified a FDA-approved drug that may sensitize resistant cancer cells by inhibiting the bioinformatically-identified aberrant molecular signals sustaining EGFR pathway activity. This network-targeting therapy, later validated in vitro/in vivo, spawned the development of our NIH Phase II clinical trial (will be p[resented in ASCO 2014). We will also provide details of a recent study aimed at associating protein domain mechanisms with Mendelian, complex and unique personal genetics.

- Clinical Grand Rounds 379 School of Medicine, Univ of Sherbrooke, Dossier médical informatisé: Introduction à l’Internet pour médecins et

chirurgiens". 6/30/1997. 380 NYPH Allen Pavilion. “Clinical Genomics.” Grand Rounds, 3/20/2003. 381 Associate Internal Medicine Clinic Meeting House Staff - Milstein Hospital, “Clinical Genomics.” New York

Presbyterian Hospital, 5/19/2003. 382 Grand Rounds, NYPH Milstein Hospital, “Clinical Genomics Technologies, Updates.” New York. Nov 2nd 2004. 383 Conf Series of General Internal Medicine of the Dept of Medicine, Columbia University. Computational Systems

Biology and Medicine: Approaches to high throughput and large scale analyses of phenotypes., 11/05/2005. 384 New York Presbyterian Hospital - Allen Pavilion, “Clinical Genomics Updates.” Grand Rounds, 7/15/2004. 385 Grand Rounds of Rheumatology, The University of Chicago, “Predicting the Molecular Underpinnings of

Complex Phenotypes with High Throughput Phenomics”, Feb 13 2007. 386 Emergency Resuscitation Center, The University of Chicago, “Computational Approaches to Unveiling Novel

Protein-Protein Interactions in Diseases”, 2/22/2007. 387 Univ of Chicago Breast Cancer Seminar, High-Throughput Analysis of Protein-Protein Interactions in Diseases”. 388 Advanced Topics in Clinical Series, Dept. of Medicine, The University of Chicago, Genomic Technologies:

clinical challenges and opportunities (6/7/2007), Proteomic Technologies (6/21/2007). 389 Liu Y, Li J, Goh C, Sam L, Gerstein M, Lussier YA. From phenotypes to genotypes: A meta-genomic approach

to uncover the molecular mechanisms of prokaryotic traits. Department of Medicine Research Day 2006. 390 Liu Y, Li j, Sam L, Lussier YA. Whole Genome Anatomics: unveiling molecular mechanisms and systems

properties of disease-related anatomies. Department of Medicine Research Day 2007. 391 Desai, Ankit A.; Moreno, Liliana; M. Gomberg-Maitland, Mardi; Maitland, Michael ; Collins, K.; Sammani,

Saad; Ma, Shwu-fan; Husain, Aliya N.; Liu, Yang; Sam, Lee; Lang, Roberto M.; Ratain, Mark J.; Lussier YA. ; Garcia JGN. Attenuation of a Rodent Model of Pulmonary Hypertension: A Novel Role for Sorafenib, a Multi-Kinase Inhibitor. Department of Medicine Research day 2007.

392 Lee Y, * Huang Y, Fan H, Wu Y, Li J, Zhang Q, Hasina R, Arakaki A, Skolnickj J, Lingen M, Weichselbaum R, Xing HR*, Lussier YA*. Novel network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. Department of Medicine Research Day, March 10, 2010.


393 “From targeted sequencing to clinically actionable transcriptomes”. University of Arizona Dept Hemato-Oncology Grand Rounds, March 27th 2014

394 Dynamic ‘omics: beyond genetic approaches to precision therapy, University of Arizona Cancer Center Grand Rounds, May 2nd 2014.

Tutorials and Workshop Presentations 395 Five SNOMED Tutorials: AMIA meetings 1995, 1996, 1997 (3), COACH 1996, 1997 (2), RA Cote, YA Lussier 400 NSIT National Institute of Standards and Technology Workshop Speaker. “Clinical Genomic Systems and Related

Clinical Standards”. Workshop on Information Technologies for Healthcare: Barriers to Implementation. Washington, 8/1/2002.

401 SFN Soc for Neuroscience Workshop Speaker. Automating Terminological Networks to Link Heterogeneous Biomedical Databases. Human Brain Project: Creating a Shared Neuroscience Ontology. 11/10/2003

402 NSF & MITRE Workshop Speaker. From Single Gene Diseases to genomic Diseases, an Informatics Perspective. Disease Modeling and Prediction workshop, 3/17/2003, McLean VA.

403 SNOMED - College of American Pathology- 6th Ann SNOMED International Users Group 9/22-24/04 404 SOFG - Standards and Ontologies for Functional Genomics Speaker. Computational Ontologies for High

Throughput Visualization and Analysis of the Phenome. 2. 9/23-26, Univ of Penn School of Medicine. 405 fMRI Data Center Summer Workshops in fMRI Informatics, Dartmouth College, 7/12-14/04. "Phenotypic

Networks and the art of Neuroinformatics" 406 IEEE/NIH/NLM Multimodal Bio-Medical Systems Workshop 2004. Bethesda, 9/22/04. 407 Knowledge-Based Bioinformatics Workshop, Ontologies, the semantic web and intelligent systems for genomics.

Concordia University. 7/21-23/05, Montreal. 408 Buffalo-Columbia Universities Workshop on Ontologies and Cancer Bioinformatics. 9/14/05 409 PSB Pac Symp Biocomput Semantic Web for Life Sciences. 2006 410 National Ctr for Ontology Research (NCOR)& AMIA KR-MED Formal Bio-Medical Know Rep 4/12/06 411 PSB Pac Symp Biocomput, Kann, Ofran, Punta, Radijovac , Lussier. Protein Interactions in Diseases. 1/4/07 412 DOD TATRC/ IEBI Advanced Technology Research Ctr Workshop on Information Extraction for Biomed Inform

(IEBI), Department of Defence Telemedicine and TATRC. 9/23/07 ↳hyperlink 413 AACR Speaker, Educational Workshop Sessions on Systems Biology of the Conference on The Science of Cancer

Health Disparities in Racial/Ethnic Minorities and the Medically Underserved and is co-sponsored by the NCI Center to Reduce Cancer Health Disparities. 9/27-30/07

414 NIH/NCI & DH&HS “The Role of Biomedical Informatics in Overcoming Current Barriers in Cancer Research, The Blackwell Inn at The Ohio State University in Columbus, Ohio, April 2-3, 2008.

415 NIH- GEI “GWAS and Other –Omics: The Need for Data Integration”, Trans-NIH Workshop – Gene Environment and Health Initiative (GEI), “Genome-wide Association: Analyze This! The Genes, Environment, and Health Initiative”. 8/4–5/08, ↳hyperlink

416 Consortium for Neuropsychiatric Phenomics “June 9, 2009” UCLA. 417 Consortium for Neuropsychiatric Phenomics, June 2010, UCLA. 418 AMIA Summit on Translational Bioinformatics 2013. Introduction to Translational Bioinformatics. ↳hyperlink 419 Translational Bioinformatics Conference 2013. Disease & drugs models with ENCODE (Encyclopedia of DNA

Elements), Oct 2, 2013.